1WO8

Crystal structure of methylglyoxal synthase from Thermus thermophilus HB8

PDB DOI: https://doi.org/10.2210/pdb1WO8/pdb

Classification: LYASE
Organism(s): Thermus thermophilus HB8
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2004-08-12 Released: 2005-08-23
Deposition Author(s): Sugahara, M., Kunishima, N., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.204
R-Value Work: 0.185
R-Value Observed: 0.186

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of methylglyoxal synthase from Thermus thermophilus HB8

Sugahara, M., Kunishima, N.

To be published.

Macromolecule Content

Total Structure Weight: 81.06 kDa
Atom Count: 6,357
Modelled Residue Count: 740
Deposited Residue Count: 756
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
methylglyoxal synthase	A, B, C, D, E A, B, C, D, E, F	126	Thermus thermophilus HB8	Mutation(s): 0 EC: 4.2.3.3
UniProt
Find proteins for Q5SHD6 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHD6 Go to UniProtKB: Q5SHD6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5SHD6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth B] SDF format, chain I [auth C] SDF format, chain J [auth D] SDF format, chain K [auth D] SDF format, chain L [auth E] SDF format, chain M [auth F] MOL2 format, chain G [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth C] MOL2 format, chain J [auth D] MOL2 format, chain K [auth D] MOL2 format, chain L [auth E] MOL2 format, chain M [auth F]	G [auth A] H [auth B] I [auth C] J [auth D] K [auth D] G [auth A], H [auth B], I [auth C], J [auth D], K [auth D], L [auth E], M [auth F]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth C] Focus chain J [auth D] Focus chain K [auth D] Focus chain L [auth E] Focus chain M [auth F] Interactions & Density Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth C] Focus chain J [auth D] Focus chain K [auth D] Focus chain L [auth E] Focus chain M [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.204
R-Value Work: 0.185
R-Value Observed: 0.186
Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 130.612	α = 90
b = 130.612	β = 90
c = 96.653	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
SOLVE	phasing
CNS	refinement
HKL-2000	data reduction

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2005-08-23

Deposition Author(s):

Sugahara, M.

Kunishima, N.

RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History (Full details and data files)

Version 1.0: 2005-08-23
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2024-03-13
Changes: Data collection, Database references, Derived calculations

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1WO8

Crystal structure of methylglyoxal synthase from Thermus thermophilus HB8

Crystal structure of methylglyoxal synthase from Thermus thermophilus HB8

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)