4WP0 | pdb_00004wp0

Crystal structure of human kynurenine aminotransferase-I with a C-terminal V5-hexahistidine tag

• PDB DOI: https://doi.org/10.2210/pdb4WP0/pdb

• Classification: Lyase, Transferase
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2014-10-17 Released: 2014-11-19 
• Deposition Author(s): Nadvi, N.A., Salam, N.K., Park, J., Akladios, F.N., Kapoor, V., Collyer, C.A., Gorrell, M.D., Church, W.B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.267 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.234 (Depositor), 0.240 (DCC) 
• R-Value Observed: 
  0.236 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of human kynurenine aminotransferase-I in a novel space group

Nadvi, N.A., Salam, N.K., Park, J., Akladios, F.N., Kapoor, V., Collyer, C.A., Gorrell, M.D., Church, W.B.

To be published.

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)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 215.29 kDa 
• Atom Count: 13,483 
• Modeled Residue Count: 1,660 
• Deposited Residue Count: 1,888 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Kynurenine--oxoglutarate transaminase 1	A, B, C, D	472	Homo sapiens	Mutation(s): 0  Gene Names: CCBL1 EC: 2.6.1.7 (PDB Primary Data), 4.4.1.13 (PDB Primary Data), 2.6.1.64 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q16773 (Homo sapiens) Explore Q16773  Go to UniProtKB:  Q16773
PHAROS:  Q16773 GTEx:  ENSG00000171097

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
LLP	A, B, C, D	L-PEPTIDE LINKING	C14 H22 N3 O7 P		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.267 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.234 (Depositor), 0.240 (DCC) 
• R-Value Observed: 0.236 (Depositor) 

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 231.15	α = 90
b = 231.15	β = 90
c = 56.105	γ = 120

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
Blu-Ice	data collection
PHENIX	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
PHASER	phasing
DENZO	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-11-19 
Deposition Author(s): Nadvi, N.A., Salam, N.K., Park, J., Akladios, F.N., Kapoor, V., Collyer, C.A., Gorrell, M.D., Church, W.B.

Revision History  

• Version 1.0: 2014-11-19
  Type: Initial release
  
• Version 1.1: 2017-05-03
  Changes: Non-polymer description
• Version 1.2: 2023-09-27
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2023-11-15
  Changes: Data collection