3CSW | pdb_00003csw

Crystal structure of a putative branched-chain amino acid aminotransferase (TM0831) from Thermotoga maritima at 2.15 A resolution

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 
    0.200 (Depositor), 0.203 (DCC) 
  • R-Value Work: 
    0.167 (Depositor), 0.171 (DCC) 
  • R-Value Observed: 
    0.168 (Depositor) 

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


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

Literature

Crystal structure of a Putative Branched-Chain Amino Acid Aminotransferase (TM0831) from Thermotoga maritima at 2.15 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content 

  • Total Structure Weight: 133.09 kDa 
  • Atom Count: 9,636 
  • Modeled Residue Count: 1,097 
  • Deposited Residue Count: 1,140 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Putative branched-chain-amino-acid aminotransferase
A, B, C, D
285Thermotoga maritima MSB8Mutation(s): 0 
Gene Names: TM0831, ilvE
EC: 2.6.1.42
UniProt
Find proteins for P74921 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8))
Explore P74921 
Go to UniProtKB:  P74921
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP74921
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PLP

Query on PLP


Download:Ideal Coordinates CCD File
E [auth A],
Q [auth C]		PYRIDOXAL-5'-PHOSPHATE
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
CIT

Query on CIT


Download:Ideal Coordinates CCD File
G [auth A],
M [auth B],
W [auth D]		CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
MPD

Query on MPD


Download:Ideal Coordinates CCD File
H [auth A]
I [auth A]
N [auth B]
O [auth B]
S [auth C]
H [auth A],
I [auth A],
N [auth B],
O [auth B],
S [auth C],
T [auth C],
X [auth D]
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
CL

Query on CL


Download:Ideal Coordinates CCD File
J [auth B],
K [auth B],
P [auth C],
U [auth D]		CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
UNL

Query on UNL


Download:Ideal Coordinates CCD File
F [auth A],
L [auth B],
R [auth C],
V [auth D]		Unknown ligand
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D
L-PEPTIDE LINKINGC5 H11 N O2 SeMET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free:  0.200 (Depositor), 0.203 (DCC) 
  • R-Value Work:  0.167 (Depositor), 0.171 (DCC) 
  • R-Value Observed: 0.168 (Depositor) 
Space Group: I 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107.71α = 90
b = 129.76β = 90
c = 298.69γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PHENIXrefinement
SHELXphasing
MolProbitymodel building
XSCALEdata scaling
PDB_EXTRACTdata extraction
MAR345data collection
XDSdata reduction
SHARPphasing
SHELXDphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-04-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Author supporting evidence, Refinement description
  • Version 1.3: 2019-07-24
    Changes: Data collection, Derived calculations, Refinement description
  • Version 1.4: 2023-02-01
    Changes: Database references, Derived calculations