1V5V

Crystal Structure of a Component of Glycine Cleavage System: T-protein from Pyrococcus horikoshii OT3 at 1.5 A Resolution

PDB DOI: https://doi.org/10.2210/pdb1V5V/pdb

Classification: TRANSFERASE
Organism(s): Pyrococcus horikoshii
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2003-11-26 Released: 2004-10-26
Deposition Author(s): Lokanath, N.K., Kunishima, N., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.209
R-Value Work: 0.197
R-Value Observed: 0.197

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of a component of glycine cleavage system: T-protein from Pyrococcus horikoshii OT3 at 1.5 A resolution

Lokanath, N.K., Kuroishi, C., Okazaki, N., Kunishima, N.

(2004) Proteins 58: 769-773

PubMed: 15609340 Search on PubMed
DOI: https://doi.org/10.1002/prot.20345
Primary Citation of Related Structures:
1V5V

Organizational Affiliation

Highthroughput Factory, RIKEN Harima Institute at SPring-8, Hyogo, Japan.

Macromolecule Content

Total Structure Weight: 92.76 kDa
Atom Count: 7,089
Modelled Residue Count: 798
Deposited Residue Count: 802
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
aminomethyltransferase	A, B	401	Pyrococcus horikoshii	Mutation(s): 0 Gene Names: GCS EC: 2.1.2.10
UniProt
Find proteins for O58888 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)) Explore O58888 Go to UniProtKB: O58888
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O58888
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain E [auth B] MOL2 format, chain E [auth B]	E [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain E [auth B] Interactions & Density Focus chain E [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B]	C [auth A], D [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.209
R-Value Work: 0.197
R-Value Observed: 0.197
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.496	α = 90
b = 96.099	β = 90
c = 118.605	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2004-10-26

Deposition Author(s):

Lokanath, N.K.

Kunishima, N.

RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History (Full details and data files)

Version 1.0: 2004-10-26
Type: Initial release
Version 1.1: 2008-04-27
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.3: 2023-12-27
Changes: Data collection, Database references, Derived calculations

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1V5V

Crystal Structure of a Component of Glycine Cleavage System: T-protein from Pyrococcus horikoshii OT3 at 1.5 A Resolution

Crystal structure of a component of glycine cleavage system: T-protein from Pyrococcus horikoshii OT3 at 1.5 A resolution

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)