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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Citation Author = "de Jong, R.M."

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Search Summary

This query matches 28 Structures.

Refinements

Structure Determination Methodology

experimental (28)

Scientific Name of Source Organism

	Piromyces sp. E2 (12)
	Agrobacterium tumefaciens (5)
	Escherichia coli K-12 (3)
	Aspergillus niger (2)
	Homo sapiens (2)
	Plasmodium falciparum (2)
	coryneform bacterium (2)
	Arthrobacter sp. AD2 (1)
	Pseudomonas pavonaceae (1)

Taxonomy

	Eukaryota (16)
	Bacteria (12)

Experimental Method

X-RAY DIFFRACTION (28)

Polymer Entity Type

Protein (28)

Refinement Resolution (Å)

	1.5 - 2.0 (14)
	2.0 - 2.5 (9)
	2.5 - 3.0 (5)

Release Date

	2000 - 2004 (4)
	2005 - 2009 (8)
	2015 - 2019 (12)
	2020 - 2024 (4)

Enzyme Classification Name

	Isomerases (13)
	Hydrolases (5)
	Lyases (2)

Symmetry Type

	Dihedral (19)
	Asymmetric (6)
	Cyclic (3)

SCOP Classification

	Alpha and beta proteins (a/b) (18)
	Alpha and beta proteins (a+b) (1)
	All beta proteins (3)

AllSelected

1 to 25 of 28 Structures

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1PWX \| pdb_00001pwx	Download File View File

Crystal structure of the haloalcohol dehalogenase HheC complexed with bromide

de Jong, R.M., Tiesinga, J.J.W., Rozeboom, H.J., Kalk, K.H., Tang, L., Janssen, D.B., Dijkstra, B.W.

(2003) EMBO J 22: 4933-4944

Released	2003-10-07
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Agrobacterium tumefaciens
Macromolecule	halohydrin dehalogenase (protein)
Unique Ligands	BR

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1PWZ \| pdb_00001pwz	Download File View File

Crystal structure of the haloalcohol dehalogenase HheC complexed with (R)-styrene oxide and chloride

de Jong, R.M., Tiesinga, J.J.W., Rozeboom, H.J., Kalk, K.H., Tang, L., Janssen, D.B., Dijkstra, B.W.

(2003) EMBO J 22: 4933-4944

Released	2003-10-07
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Agrobacterium tumefaciens
Macromolecule	halohydrin dehalogenase (protein)
Unique Ligands	CL, RSO

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1PX0 \| pdb_00001px0	Download File View File

Crystal structure of the haloalcohol dehalogenase HheC complexed with the haloalcohol mimic (R)-1-para-nitro-phenyl-2-azido-ethanol

de Jong, R.M., Tiesinga, J.J.W., Rozeboom, H.J., Kalk, K.H., Tang, L., Janssen, D.B., Dijkstra, B.W.

(2003) EMBO J 22: 4933-4944

Released	2003-10-07
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Agrobacterium tumefaciens
Macromolecule	halohydrin dehalogenase (protein)
Unique Ligands	RPN

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1S0Y \| pdb_00001s0y	Download File View File

The structure of trans-3-chloroacrylic acid dehalogenase, covalently inactivated by the mechanism-based inhibitor 3-bromopropiolate at 2.3 Angstrom resolution

de Jong, R.M., Brugman, W., Poelarends, G.J., Whitman, C.P., Dijkstra, B.W.

(2004) J Biological Chem 279: 11546-11552

Released	2004-02-24
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Pseudomonas pavonaceae
Macromolecule	alpha-subunit of trans-3-chloroacrylic acid dehalogenase (protein) beta-subunit of trans-3-chloroacrylic acid dehalogenase (protein)
Unique Ligands	MLA

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1ZMO \| pdb_00001zmo	Download File View File

Apo structure of haloalcohol dehalogenase HheA of Arthrobacter sp. AD2

de Jong, R.M., Kalk, K.H., Tang, L., Janssen, D.B., Dijkstra, B.W.

(2006) J Bacteriol 188: 4051-4056

Released	2006-04-25
Method	X-RAY DIFFRACTION 2 Å
Organisms	Arthrobacter sp. AD2
Macromolecule	halohydrin dehalogenase (protein)

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1ZMT \| pdb_00001zmt	Download File View File

Structure of haloalcohol dehalogenase HheC of Agrobacterium radiobacter AD1 in complex with (R)-para-nitro styrene oxide, with a water molecule in the halide-binding site

de Jong, R.M., Tiesinga, J.J.W., Villa, A., Tang, L., Janssen, D.B., Dijkstra, B.W.

(2005) J Am Chem Soc 127: 13338-13343

Released	2005-10-04
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Agrobacterium tumefaciens
Macromolecule	Haloalcohol dehalogenase HheC (protein)
Unique Ligands	RNO

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1ZO8 \| pdb_00001zo8	Download File View File

X-ray Structure of the haloalcohol dehalogenase HheC of Agrobacterium radiobacter AD1 in complex with (S)-para-nitrostyrene oxide, with a water molecule in the halide-binding site

de Jong, R.M., Tiesinga, J.J.W., Tang, L., Villa, A., Janssen, D.B., Dijkstra, B.W.

(2005) J Am Chem Soc 127: 13338-13343

Released	2005-10-04
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Agrobacterium tumefaciens
Macromolecule	halohydrin dehalogenase (protein)
Unique Ligands	SNO

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2FLT \| pdb_00002flt	Download File View File

The X-ray structure of the cis-3-chloroacrylic acid dehalogenase cis-CaaD inactivated with (R)-Oxirane-2-carboxylate

de Jong, R.M.

(2007) J Biological Chem 282: 2440-2449

Released	2006-11-21
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	coryneform bacterium
Macromolecule	cis-3-chloroacrylic acid dehalogenase (protein)
Unique Ligands	LAC

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2FLZ \| pdb_00002flz	Download File View File

The X-ray structure of cis-3-chloroacrylic acid dehalogenase (cis-CaaD) with a sulfate ion bound in the active site

de Jong, R.M.

(2007) J Biological Chem 282: 2440-2449

Released	2006-11-21
Method	X-RAY DIFFRACTION 2.75 Å
Organisms	coryneform bacterium
Macromolecule	cis-3-chloroacrylic acid dehalogenase (protein)
Unique Ligands	SO4

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2PI8 \| pdb_00002pi8	Download File View File

Crystal structure of E. coli MltA with bound chitohexaose

van Straaten, K.E., Barends, T.R.M., Dijkstra, B.W., Thunnissen, A.M.W.H.

(2007) J Biological Chem 282: 21197-21205

Released	2007-05-08
Method	X-RAY DIFFRACTION 2.25 Å
Organisms	Escherichia coli K-12
Macromolecule	Membrane-bound lytic murein transglycosylase A (protein)
Unique Ligands	PO4
Unique branched monosaccharides	NAG

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2PIC \| pdb_00002pic	Download File View File

E. coli lytic transglycosylase MltA-D308A in apo-2 form

van Straaten, K.E., Dijkstra, B.W., Thunnissen, A.M.W.H.

(2007) J Biological Chem 282: 21197-21205

Released	2007-05-08
Method	X-RAY DIFFRACTION 2.25 Å
Organisms	Escherichia coli K-12
Macromolecule	Membrane-bound lytic murein transglycosylase A (protein)

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2PJJ \| pdb_00002pjj	Download File View File

E. coli lytic transglycosylase MltA-D308A in apo-1 form

van Straaten, K.E., Dijkstra, B.W., Thunnissen, A.M.W.H.

(2007) J Biological Chem 282: 21197-21205

Released	2007-05-08
Method	X-RAY DIFFRACTION 2.46 Å
Organisms	Escherichia coli K-12
Macromolecule	Membrane-bound lytic murein transglycosylase A (protein)

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5NH4 \| pdb_00005nh4	Download File View File

Crystal structure of xylose isomerase from Piromyces E2 in complex with one Mg2+ ions and glycerol

Rozeboom, H.J., Janssen, D.B.

(2017) Biochemistry 56: 5991-6005

Released	2017-11-01
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Piromyces sp. E2
Macromolecule	Xylose isomerase (protein)
Unique Ligands	GOL, MG, SO4

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5NH5 \| pdb_00005nh5	Download File View File

Crystal structure of native xylose isomerase from Piromyces E2

Rozeboom, H.J., Janssen, D.B.

(2017) Biochemistry 56: 5991-6005

Released	2017-11-01
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Piromyces sp. E2
Macromolecule	Xylose isomerase (protein)
Unique Ligands	CA, FE2, GOL, MG, SO4

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5NH6 \| pdb_00005nh6	Download File View File

Crystal structure of xylose isomerase from Piromyces E2 Complexed with one Mg2+ ion and xylitol

Rozeboom, H.J., Janssen, D.B.

(2017) Biochemistry 56: 5991-6005

Released	2017-11-01
Method	X-RAY DIFFRACTION 1.75 Å
Organisms	Piromyces sp. E2
Macromolecule	Xylose isomerase (protein)
Unique Ligands	MG, SO4, XYL

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5NH7 \| pdb_00005nh7	Download File View File

Crystal structure of xylose isomerase from Piromyces E2 in complex with two Mg2+ ions and xylose

Rozeboom, H.J., Janssen, D.B.

(2017) Biochemistry 56: 5991-6005

Released	2017-11-01
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Piromyces sp. E2
Macromolecule	Xylose isomerase (protein)
Unique Ligands	MG, SO4, XLS, XYP, XYS

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5NH8 \| pdb_00005nh8	Download File View File

Crystal structure of xylose isomerase from Piromyces E2 in complex with two Ca2+ ions and xylose

Rozeboom, H.J., Janssen, D.B.

(2017) Biochemistry 56: 5991-6005

Released	2017-11-01
Method	X-RAY DIFFRACTION 1.86 Å
Organisms	Piromyces sp. E2
Macromolecule	Xylose isomerase (protein)
Unique Ligands	CA, SO4, XLS, XYP

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5NH9 \| pdb_00005nh9	Download File View File

Crystal structure of xylose isomerase from Piromyces E2 in complex with two Mn2+ ions and xylose

Rozeboom, H.J., Janssen, D.B.

(2017) Biochemistry 56: 5991-6005

Released	2017-11-01
Method	X-RAY DIFFRACTION 2.08 Å
Organisms	Piromyces sp. E2
Macromolecule	Xylose isomerase (protein)
Unique Ligands	MN, SO4, XLS, XYP

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5NHA \| pdb_00005nha	Download File View File

Crystal structure of xylose isomerase from Piromyces sp. E2 in complex with two Mn2+ ions and sorbitol

Rozeboom, H.J., Janssen, D.B.

(2017) Biochemistry 56: 5991-6005

Released	2017-11-01
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Piromyces sp. E2
Macromolecule	Xylose isomerase (protein)
Unique Ligands	MN, SO4, SOR

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5NHB \| pdb_00005nhb	Download File View File

Crystal structure of xylose isomerase from Piromyces E2 in complex with two Fe2+ ions

Rozeboom, H.J., Janssen, D.B.

(2017) Biochemistry 56: 5991-6005

Released	2017-11-01
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Piromyces sp. E2
Macromolecule	Xylose isomerase (protein)
Unique Ligands	FE2, SO4

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5NHC \| pdb_00005nhc	Download File View File

Crystal structure of xylose isomerase from Piromyces E2 in complex with two Co2+ ions and xylulose

Rozeboom, H.J., Janssen, D.B.

(2017) Biochemistry 56: 5991-6005

Released	2017-11-01
Method	X-RAY DIFFRACTION 1.93 Å
Organisms	Piromyces sp. E2
Macromolecule	Xylose isomerase (protein)
Unique Ligands	CO, HYP, XUL

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5NHD \| pdb_00005nhd	Download File View File

Crystal structure of xylose isomerase from Piromyces E2 in complex with 2 Ni2+ ions and xylose

Rozeboom, H.J., Janssen, D.B.

(2017) Biochemistry 56: 5991-6005

Released	2017-11-01
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Piromyces sp. E2
Macromolecule	Xylose isomerase (protein)
Unique Ligands	NI, SO4, XLS, XYP, XYS

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5NHE \| pdb_00005nhe	Download File View File

Crystal structure of xylose isomerase from Piromyces E2 in complex with two Cd2+ ions and xylose

Rozeboom, H.J., Janssen, D.B.

(2017) Biochemistry 56: 5991-6005

Released	2017-11-01
Method	X-RAY DIFFRACTION 1.86 Å
Organisms	Piromyces sp. E2
Macromolecule	Xylose isomerase (protein)
Unique Ligands	CD, SO4, XLS, XYP, XYS

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5NHM \| pdb_00005nhm	Download File View File

Crystal structure of apo xylose isomerase from Piromyces E2

Rozeboom, H.J., Janssen, D.B.

(2017) Biochemistry 56: 5991-6005

Released	2017-11-01
Method	X-RAY DIFFRACTION 1.67 Å
Organisms	Piromyces sp. E2
Macromolecule	Xylose isomerase (protein)
Unique Ligands	ACY, GOL, SO4

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7UXL \| pdb_00007uxl	Download File View File

Crystal structure of malaria transmission-blocking antigen Pfs48/45-6C variant in complex with human antibodies RUPA-44 and RUPA-29

Hailemariam, S., Ivanochko, D., Julien, J.P.

(2023) Immunity 56: 406-419.e7

Released	2023-02-15
Method	X-RAY DIFFRACTION 2.86 Å
Organisms	Homo sapiens Plasmodium falciparum
Macromolecule	Gametocyte surface protein P45/48 (protein) RUPA-29 Fab Heavy chain (protein) RUPA-29 Fab Lambda chain (protein) RUPA-44 Fab Heavy chain (protein) RUPA-44 Fab Kappa chain (protein)
Unique Ligands	NAG

1 to 25 of 28 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

1PWX | pdb_00001pwx

1PWZ | pdb_00001pwz

1PX0 | pdb_00001px0

1S0Y | pdb_00001s0y

1ZMO | pdb_00001zmo

1ZMT | pdb_00001zmt

1ZO8 | pdb_00001zo8

2FLT | pdb_00002flt

2FLZ | pdb_00002flz

2PI8 | pdb_00002pi8

2PIC | pdb_00002pic

2PJJ | pdb_00002pjj

5NH4 | pdb_00005nh4

5NH5 | pdb_00005nh5

5NH6 | pdb_00005nh6

5NH7 | pdb_00005nh7

5NH8 | pdb_00005nh8

5NH9 | pdb_00005nh9

5NHA | pdb_00005nha

5NHB | pdb_00005nhb

5NHC | pdb_00005nhc

5NHD | pdb_00005nhd

5NHE | pdb_00005nhe

5NHM | pdb_00005nhm

7UXL | pdb_00007uxl