RCSB PDB - 9J32: Crystal structure of aminotransferase-like protein from Variovorax paradoxus mutant N174K

 9J32

Crystal structure of aminotransferase-like protein from Variovorax paradoxus mutant N174K


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.217 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Protein of unknown function from variovorax paradoxus with amino acid substitution n174k is able to form schiff base with plp molecule

Ilyasov, I.Minyaev, M.Rakitina, T.Bakunova, A.Popov, V.Bezsudnova, E.Boyko, K.

(2024) Кристаллография 69: 981-986


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Aminotransferase, class 4
A, B, C
317Variovorax paradoxus B4Mutation(s): 1 
Gene Names: VAPA_1c54540
EC: 2.6.1.42
UniProt
Find proteins for T1XIY1 (Variovorax paradoxus B4)
Explore T1XIY1 
Go to UniProtKB:  T1XIY1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupT1XIY1
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PEG
Query on PEG

Download Ideal Coordinates CCD File 
D [auth C]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
LLP
Query on LLP
A, B, C
L-PEPTIDE LINKINGC14 H22 N3 O7 PLYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.217 
  • Space Group: I 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.245α = 90
b = 87.34β = 99.45
c = 104.655γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Higher Education of the Russian FederationRussian Federation075-15-2021-1354

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-29
    Type: Initial release
  • Version 1.1: 2025-02-05
    Changes: Database references