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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free:
0.267 (Depositor), 0.257 (DCC)
R-Value Work:
0.234 (Depositor), 0.233 (DCC)
R-Value Observed:
0.236 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 4WP0

This is version 1.3 of the entry. See complete history.

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.

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

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q16773
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
LLP Query on 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), 0.257 (DCC)
R-Value Work: 0.234 (Depositor), 0.233 (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

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Entry History

Deposition Data

Released Date: 2014-11-19

Deposition Author(s):

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.