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)

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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 

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 
• DOI: https://doi.org/10.1002/prot.20345
• Primary Citation of Related Structures:  
  1V5V

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

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

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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	E [auth B]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL	C [auth A], D [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

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

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  

• 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