1VP4

Crystal structure of a putative aminotransferase (tm1131) from thermotoga maritima msb8 at 1.82 A resolution

• PDB DOI:  https://doi.org/10.2210/pdb1VP4/pdb

• Classification: TRANSFERASE
• Organism(s): Thermotoga maritima MSB8
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2004-10-08 Released: 2004-10-26 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.82 Å
• R-Value Free: 0.203 
• R-Value Work: 0.179 
• R-Value Observed: 0.180 

Literature

Crystal structure of Aminotransferase, putative (TM1131) from Thermotoga maritima at 1.82 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 100.27 kDa 
• Atom Count: 7,074 
• Modelled Residue Count: 836 
• Deposited Residue Count: 850 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
aminotransferase, putative	A, B	425	Thermotoga maritima MSB8	Mutation(s): 8  Gene Names: TM1131, TM_1131
UniProt
Find proteins for Q9X0L5 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9X0L5  Go to UniProtKB:  Q9X0L5

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PLP	C [auth A], Z [auth B]	PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N
EDO	BA [auth B], CA [auth B], DA [auth B], E [auth A], F [auth A], G [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
FMT	EA [auth B], FA [auth B], GA [auth B], H [auth A], HA [auth B], I [auth A], IA [auth B], J [auth A], JA [auth B], K [auth A], KA [auth B], L [auth A], LA [auth B], M [auth A], MA [auth B], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A], S [auth A], T [auth A], U [auth A], V [auth A], W [auth A], X [auth A], Y [auth A]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N
UNL	AA [auth B], D [auth A]	Unknown ligand BDAGIHXWWSANSR-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.82 Å
• R-Value Free: 0.203 
• R-Value Work: 0.179 
• R-Value Observed: 0.180 
• Space Group: P 6₅
• Diffraction Data: https://doi.org/10.18430/M31VP4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 165.125	α = 90
b = 165.125	β = 90
c = 68.701	γ = 120

Software Package:

Software Name	Purpose
XDSauto	data collection
SCALA	data scaling
SHELX	model building
SHARP	phasing
REFMAC	refinement
XDS	data reduction
CCP4	data scaling
SHELX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-10-26 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2004-10-26
  Type: Initial release
  
• Version 1.1: 2008-04-26
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Source and taxonomy, Version format compliance
• Version 1.3: 2023-01-25
  Changes: Database references, Derived calculations