2DSH | pdb_00002dsh

Crystal structure of Lys26 to Tyr mutant of Diphthine synthase

PDB DOI: https://doi.org/10.2210/pdb2DSH/pdb

Classification: TRANSFERASE
Organism(s): Pyrococcus horikoshii OT3
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2006-06-30 Released: 2006-12-30
Deposition Author(s): Mizutani, H., Matsuura, Y., Saraboji, K., Malathy Sony, S.M., Ponnuswamy, M.N., Kumarevel, T.S., Kunishima, N., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.218 (Depositor), 0.210 (DCC)
R-Value Work:
0.194 (Depositor), 0.190 (DCC)
R-Value Observed:
0.194 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Crystal structure of diphthine synthase from Pyrococcus horikoshii OT3

Mizutani, H., Matsuura, Y., Saraboji, K., Malathy Sony, S.M., Ponnuswamy, M.N., Kumarevel, T.S., Kunishima, N.

To be published.

Macromolecule Content

Total Structure Weight: 61.21 kDa
Atom Count: 4,803
Modelled Residue Count: 530
Deposited Residue Count: 530
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
diphthine synthase	A, B	265	Pyrococcus horikoshii OT3	Mutation(s): 1 Gene Names: dphB EC: 2.1.1.98
UniProt
Find proteins for O58456 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)) Explore O58456 Go to UniProtKB: O58456
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O58456
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SAH Query on SAH Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	S-ADENOSYL-L-HOMOCYSTEINE C₁₄ H₂₀ N₆ O₅ S ZJUKTBDSGOFHSH-WFMPWKQPSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
MES Query on MES Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain N [auth B] SDF format, chain O [auth B] MOL2 format, chain G [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] mmCIF format, chain G [auth A] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B]	G [auth A], N [auth B], O [auth B]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain N [auth B] Focus chain O [auth B] Interactions & Density Focus chain G [auth A] Focus chain N [auth B] Focus chain O [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B]	C [auth A] D [auth A] E [auth A] J [auth B] K [auth B] C [auth A], D [auth A], E [auth A], J [auth B], K [auth B], L [auth B], M [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain P [auth B] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain P [auth B] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain P [auth B]	H [auth A], I [auth A], P [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain P [auth B] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain P [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.218 (Depositor), 0.210 (DCC)
R-Value Work: 0.194 (Depositor), 0.190 (DCC)
R-Value Observed: 0.194 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.777	α = 90
b = 104.777	β = 90
c = 135.844	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2006-12-30

Deposition Author(s):

RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History (Full details and data files)

Version 1.0: 2006-12-30
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Source and taxonomy, Version format compliance
Version 1.3: 2021-11-10
Changes: Database references, Derived calculations
Version 1.4: 2023-10-25
Changes: Data collection, Refinement description