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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Structure Author = "Boer, D.R."

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Search Summary

This query matches 34 Structures.

Refinements

Structure Determination Methodology

experimental (34)

Scientific Name of Source Organism

	Streptococcus agalactiae (9)
	Arabidopsis thaliana (7)
	Bacillus subtilis subsp. natto (3)
	Escherichia coli K-12 (3)
	Marchantia polymorpha (3)
	Bacillus subtilis (2)
	Homo sapiens (2)
	Megalodesulfovibrio gigas (2)
	synthetic construct (2)
	Bacillus altitudinis (1)

More...

Taxonomy

	Bacteria (20)
	Eukaryota (11)
	other sequences (3)

Experimental Method

X-RAY DIFFRACTION (34)

Polymer Entity Type

	Protein (31)
	DNA (17)

Refinement Resolution (Å)

	1.0 - 1.5 (4)
	1.5 - 2.0 (6)
	2.0 - 2.5 (9)
	2.5 - 3.0 (10)
	3.0 - 3.5 (3)
	3.5 - 4.0 (2)

Release Date

	2000 - 2004 (1)
	2005 - 2009 (2)
	2010 - 2014 (14)
	2015 - 2019 (4)
	2020 - 2024 (13)

Enzyme Classification Name

	Oxidoreductases (2)
	Ligases (1)
	Transferases (1)

Symmetry Type

	Cyclic (17)
	Asymmetric (12)
	Dihedral (3)

SCOP Classification

	Alpha and beta proteins (a+b) (2)
	All alpha proteins (2)

AllSelected

1 to 25 of 34 Structures

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1SIJ \| pdb_00001sij	Download File View File

Crystal structure of the Aldehyde Dehydrogenase (a.k.a. AOR or MOP) of Desulfovibrio gigas covalently bound to [AsO3]-

Boer, D.R., Thapper, A., Brondino, C.D., Romao, M.J., Moura, J.J.G.

(2004) J Am Chem Soc 126: 8614-8615

Released	2004-07-27
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Megalodesulfovibrio gigas
Macromolecule	Aldehyde oxidoreductase (protein)
Unique Ligands	AST, CL, FES, MG, PCD

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3DKX \| pdb_00003dkx	Download File View File

Crystal Structure of the replication initiator protein encoded on plasmid pMV158 (RepB), trigonal form, to 2.7 Ang resolution

Boer, D.R., Ruiz-Maso, J.A., Blanco, A.G., Vives-Llacer, M., Uson, I., Gomis-Ruth, F.X., Espinosa, M., Del Solar, G., Coll, M.

(2009) EMBO J 28: 1666-1678

Released	2009-06-30
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	Streptococcus agalactiae
Macromolecule	Replication protein repB (protein)
Unique Ligands	CL, MG, MN

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3DKY \| pdb_00003dky	Download File View File

Crystal Structure of the replication initiator protein encoded on plasmid pMV158 (RepB), tetragonal form, to 3.6 Ang resolution

Boer, D.R., Ruiz-Maso, J.A., Blanco, A.G., Vives-Llacer, M., Uson, I., Gomis-Ruth, F.X., Espinosa, M., Del Solar, G., Coll, M.

(2009) EMBO J 28: 1666-1678

Released	2009-06-30
Method	X-RAY DIFFRACTION 3.6 Å
Organisms	Streptococcus agalactiae
Macromolecule	Replication protein repB (protein)
Unique Ligands	MN

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3FX8 \| pdb_00003fx8	Download File View File

Distinct recognition of three-way DNA junctions by a thioester variant of a metallo-supramolecular cylinder ('helicate')

Boer, D.R., Uson, I., Coll, M.

(2010) Angew Chem Int Ed Engl 49: 2336-2339

Released	2010-03-16
Method	X-RAY DIFFRACTION 2.44 Å
Macromolecule	(5'-D(CPGPTPAPCPG)-3' (nucleic acid)
Unique Ligands	5PM, FE2

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3I1D \| pdb_00003i1d	Download File View File

Distinct recognition of three-way DNA junctions by the two enantiomers of a metallo-supramolecular cylinder ('helicate')

Boer, D.R., Uson, I., Hannon, M.J., Coll, M.

(2010) Angew Chem Int Ed Engl 49: 2336-2339

Released	2011-01-12
Method	X-RAY DIFFRACTION 2.5 Å
Macromolecule	5'-D(CPGPTPAPCPG)-3' (nucleic acid)
Unique Ligands	FE2, NPM

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3L4P \| pdb_00003l4p	Download File View File

Crystal structure of the Aldehyde Dehydrogenase (a.k.a. AOR or MOP) of Desulfovibrio gigas covalently bound to [AsO3]-

Boer, D.R., Romao, M.J.

(2007) J Biol Inorg Chem 12: 353-366

Released	2010-02-16
Method	X-RAY DIFFRACTION 1.45 Å
Organisms	Megalodesulfovibrio gigas
Macromolecule	Aldehyde oxidoreductase (protein)
Unique Ligands	AST, CA, CL, FES, IPA, LI, MG, PCD, URE

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4GQJ \| pdb_00004gqj	Download File View File

Complex of a binuclear Ruthenium compound D,D-([mu-(11,11')-bi(dppz)-(1,10-phenanthroline)4-Ru2]4+) bound to d(CGTACG)

Boer, D.R., Coll, M.

(2014) Angew Chem Int Ed Engl 53: 1949-1952

Released	2014-03-05
Method	X-RAY DIFFRACTION 2.951 Å
Macromolecule	DNA (5'-D(CPGPTPAPCPG)-3') (nucleic acid)
Unique Ligands	RR2

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4LDU \| pdb_00004ldu	Download File View File

Crystal structure of the DNA binding domain of Arabidopsis thaliana auxin response factor 5

Boer, D.R., Freire-Rios, A., van den Berg, W.M.A., Weijers, D., Coll, M.

(2014) Cell 156: 577-589

Released	2014-02-12
Method	X-RAY DIFFRACTION 2.15 Å
Organisms	Arabidopsis thaliana
Macromolecule	Auxin response factor 5 (protein)
Unique Ligands	CL

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4LDV \| pdb_00004ldv	Download File View File

Crystal structure of the DNA binding domain of A. thailana auxin response factor 1

boer, D.R., Freire-Rios, A., van den Berg, W.M.A., Weijers, D., Coll, M.

(2014) Cell 156: 577-589

Released	2014-02-12
Method	X-RAY DIFFRACTION 1.45 Å
Organisms	Arabidopsis thaliana
Macromolecule	Auxin response factor 1 (protein)
Unique Ligands	CL, FMT, IOD

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4LDW \| pdb_00004ldw	Download File View File

Crystal structure of the DNA Binding Domain of arabidopsis thaliana auxin response factor 1, P21 structure

boer, D.R., Coll, M.

(2014) Cell 156: 577-589

Released	2014-02-12
Method	X-RAY DIFFRACTION 2.67 Å
Organisms	Arabidopsis thaliana
Macromolecule	Auxin response factor 1 (protein)
Unique Ligands	CL

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4LDX \| pdb_00004ldx	Download File View File

Crystal structure of the DNA binding domain of arabidopsis thaliana auxin response factor 1 (ARF1) in complex with protomor-like sequence ER7

Boer, D.R., Freire-Rios, A., van den Berg, W.M.A., Weijers, D., Coll, M.

(2014) Cell 156: 577-589

Released	2014-02-12
Method	X-RAY DIFFRACTION 2.9 Å
Organisms	Arabidopsis thaliana
Macromolecule	Auxin response factor 1 (protein) ER7, forward sequence (nucleic acid) ER7, reverse sequence (nucleic acid)

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4LDY \| pdb_00004ldy	Download File View File

Crystal structure of the DNA binding domain of the G245A mutant of arabidopsis thaliana auxin reponse factor 1

Boer, D.R., Freire-Rios, A., van den Berg, W.M.A., Weijers, D., Coll, M.

(2014) Cell 156: 577-589

Released	2014-02-12
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Arabidopsis thaliana
Macromolecule	Auxin response factor 1 (protein)
Unique Ligands	CL

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4LVI \| pdb_00004lvi	Download File View File

MobM Relaxase Domain (MOBV; Mob_Pre) bound to plasmid pMV158 oriT DNA (22nt). Mn-bound crystal structure at pH 4.6

Pluta, R., Boer, D.R., Coll, M.

(2017) Proc Natl Acad Sci U S A 114: E6526-E6535

Released	2014-09-24
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Streptococcus agalactiae
Macromolecule	Plasmid recombination enzyme (protein) ACTTTAT oligonucleotide (nucleic acid) ATAAAGTATAGTGTG oligonucleotide (nucleic acid)
Unique Ligands	GOL, MN

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4LVJ \| pdb_00004lvj	Download File View File

MobM Relaxase Domain (MOBV; Mob_Pre) bound to plasmid pMV158 oriT DNA (22nt). Mn-bound crystal structure at pH 5.5

Pluta, R., Boer, D.R., Coll, M.

(2017) Proc Natl Acad Sci U S A 114: E6526-E6535

Released	2014-09-24
Method	X-RAY DIFFRACTION 2.17 Å
Organisms	Streptococcus agalactiae
Macromolecule	Plasmid recombination enzyme (protein) ACTTTAT oligonucleotide (nucleic acid) ATAAAGTATAGTGTG oligonucleotide (nucleic acid)
Unique Ligands	ACT, MN

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4LVK \| pdb_00004lvk	Download File View File

MobM Relaxase Domain (MOBV; Mob_Pre) bound to plasmid pMV158 oriT DNA (22nt+3'Phosphate). Mn-bound crystal structure at pH 4.6

Pluta, R., Boer, D.R., Coll, M.

(2017) Proc Natl Acad Sci U S A 114: E6526-E6535

Released	2014-09-24
Method	X-RAY DIFFRACTION 2.37 Å
Organisms	Streptococcus agalactiae
Macromolecule	Plasmid recombination enzyme (protein) ACTTTAT oligonucleotide (nucleic acid) ATAAAGTATAGTGTGpo oligonucleotide (nucleic acid)
Unique Ligands	MN, NA

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4LVL \| pdb_00004lvl	Download File View File

MobM Relaxase Domain (MOBV; Mob_Pre) bound to plasmid pMV158 oriT DNA (22nt+3'Thiophosphate). Mn-bound crystal structure at pH 6.8

Pluta, R., Boer, D.R., Coll, M.

(2017) Proc Natl Acad Sci U S A 114: E6526-E6535

Released	2014-09-24
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Streptococcus agalactiae synthetic construct
Macromolecule	Plasmid recombination enzyme (protein) DNA (5'-D(APCPTPTPTPAPT)-3') (nucleic acid) DNA (5'-D(APTPAPAPAPGPTPAPTPAPGPTPGPTPGP*(TS6))-3') (nucleic acid)
Unique Ligands	CL, MN

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4LVM \| pdb_00004lvm	Download File View File

MobM Relaxase Domain (MOBV; Mob_Pre) bound to plasmid pMV158 oriT DNA (23nt). Mn-bound crystal structure at pH 6.5

Pluta, R., Boer, D.R., Coll, M.

(2017) Proc Natl Acad Sci U S A 114: E6526-E6535

Released	2014-09-24
Method	X-RAY DIFFRACTION 3.1 Å
Organisms	Streptococcus agalactiae
Macromolecule	Plasmid recombination enzyme (protein) ACTTTAT oligonucleotide (nucleic acid) ATAAAGTATAGTGTGT oligonucleotide (nucleic acid)
Unique Ligands	CL, MG, MN, NA

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4U87 \| pdb_00004u87	Download File View File

Crystal structure of the Ba-soaked C2 crystal form of pMV158 replication initiator RepB (P3221 space group)

Boer, D.R., Ruiz Maso, J.A., del Solar, G., Coll, M.

(2016) Sci Rep 6: 20915-20915

Released	2015-08-26
Method	X-RAY DIFFRACTION 3.8 Å
Organisms	Streptococcus agalactiae
Macromolecule	Replication protein RepB (protein)
Unique Ligands	BA, CL, MN

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5DKA \| pdb_00005dka	Download File View File

A C2HC zinc finger is essential for the activity of the RING ubiquitin ligase RNF125

Boer, D.R., Coll, M., Bijlmakers, M.J.

(2016) Sci Rep 6: 29232-29232

Released	2016-07-27
Method	X-RAY DIFFRACTION 1.55 Å
Organisms	Homo sapiens
Macromolecule	E3 ubiquitin-protein ligase RNF125 (protein)
Unique Ligands	CL, MG, ZN

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5N2Q \| pdb_00005n2q	Download File View File

MobM Relaxase Domain (MOBV; Mob_Pre) bound to 26nt pMV158 oriT DNA

Russi, S., Boer, D.R., Coll, M.

(2017) Proc Natl Acad Sci U S A 114: E6526-E6535

Released	2017-04-12
Method	X-RAY DIFFRACTION 2 Å
Organisms	Plasmid pMV158 Streptococcus agalactiae
Macromolecule	Plasmid recombination enzyme (protein) DNA (26-MER) (nucleic acid)
Unique Ligands	CL, GOL, MG, NA

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6GYG \| pdb_00006gyg	Download File View File

X-ray structure of the apo form of the establishement gene regulator Reg576 of the G+ plasmid p576

Crespo, I., Meijer, W.J.J., Boer, D.R.

(2018) Nucleic Acids Res 46: 11910-11926

Released	2018-10-17
Method	X-RAY DIFFRACTION 1.98 Å
Organisms	Bacillus altitudinis
Macromolecule	Transcription regulator Reg576 (protein)

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6SDG \| pdb_00006sdg	Download File View File

Crystal structure of the DNA binding domain of M. polymorpha Auxin Response Factor 2 (MpARF2) in complex with High Affinity DNA

Crespo, I., Weijers, D., Boer, D.R.

(2020) Nat Plants 6: 473-482

Released	2020-04-08
Method	X-RAY DIFFRACTION 2.96 Å
Organisms	Arabidopsis thaliana Marchantia polymorpha
Macromolecule	Auxin response factor (protein) 21-7_A (nucleic acid) 21-7_B (nucleic acid)

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6T3H \| pdb_00006t3h	Download File View File

Structure of the Rap conjugation gene regulator of the plasmid pLS20 in apo form

Crespo, I., Bernardo, N., Meijer, W.J.J., Boer, D.R.

(2020) Nucleic Acids Res 48: 8113-8127

Released	2020-06-24
Method	X-RAY DIFFRACTION 3.039 Å
Organisms	Bacillus subtilis subsp. natto
Macromolecule	Response regulator aspartate phosphatase (protein)

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6T46 \| pdb_00006t46	Download File View File

Structure of the Rap conjugation gene regulator of the plasmid pLS20 in complex with the Phr* peptide

Crespo, I., Bernardo, N., Meijer, W.J.J., Boer, D.R.

(2020) Nucleic Acids Res 48: 8113-8127

Released	2020-06-24
Method	X-RAY DIFFRACTION 2.45 Å
Organisms	Bacillus subtilis subsp. natto
Macromolecule	Quorum-sensing secretion protein (processed) (protein) Response regulator aspartate phosphatase (protein)
Unique Ligands	CL, NA

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6YCQ \| pdb_00006ycq	Download File View File

Crystal structure of the DNA binding domain of Arabidopsis thaliana Auxin Response Factor 1 (AtARF1) in complex with High Affinity DNA

Crespo, I., Weijers, D., Boer, D.R.

(2020) Proc Natl Acad Sci U S A 117: 24557-24566

Released	2020-09-09
Method	X-RAY DIFFRACTION 1.65 Å
Organisms	Arabidopsis thaliana
Macromolecule	Auxin response factor 1 (protein) 21-7A (nucleic acid) 21-7B (nucleic acid)
Unique Ligands	CL, FMT, NA, TRS

1 to 25 of 34 Structures

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Structure Determination Methodology

Scientific Name of Source Organism

Taxonomy

Experimental Method

Polymer Entity Type

Refinement Resolution (Å)

Release Date

Enzyme Classification Name

Symmetry Type

SCOP Classification

1SIJ | pdb_00001sij

3DKX | pdb_00003dkx

3DKY | pdb_00003dky

3FX8 | pdb_00003fx8

3I1D | pdb_00003i1d

3L4P | pdb_00003l4p

4GQJ | pdb_00004gqj

4LDU | pdb_00004ldu

4LDV | pdb_00004ldv

4LDW | pdb_00004ldw

4LDX | pdb_00004ldx

4LDY | pdb_00004ldy

4LVI | pdb_00004lvi

4LVJ | pdb_00004lvj

4LVK | pdb_00004lvk

4LVL | pdb_00004lvl

4LVM | pdb_00004lvm

4U87 | pdb_00004u87

5DKA | pdb_00005dka

5N2Q | pdb_00005n2q

6GYG | pdb_00006gyg

6SDG | pdb_00006sdg

6T3H | pdb_00006t3h

6T46 | pdb_00006t46

6YCQ | pdb_00006ycq