5V28 | pdb_00005v28

2.72 angstrom crystal structure of P97A 3-hydroxyanthranilate-3,4-dioxygenase from Cupriavidus metallidurans

PDB DOI: https://doi.org/10.2210/pdb5V28/pdb

Classification: OXIDOREDUCTASE
Organism(s): Cupriavidus metallidurans CH34
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2017-03-02 Released: 2018-03-07
Deposition Author(s): Dornevil, K., Liu, F., Liu, A.
Funding Organization(s): National Science Foundation (NSF, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.72 Å
R-Value Free:
0.262 (Depositor), 0.260 (DCC)
R-Value Work:
0.192 (Depositor), 0.190 (DCC)
R-Value Observed:
0.196 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

2.72 angstrom crystal structure of P97A 3-hydroxyanthranilate-3,4-dioxygenase from Cupriavidus metallidurans

Dornevil, K., Liu, F., Liu, A.

To be published.

Macromolecule Content

Total Structure Weight: 23.29 kDa
Atom Count: 1,427
Modeled Residue Count: 174
Deposited Residue Count: 201
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-hydroxyanthranilate 3,4-dioxygenase	A	201	Cupriavidus metallidurans CH34	Mutation(s): 1 Gene Names: nbaC, Rmet_5193 EC: 1.13.11.6
UniProt
Find proteins for Q1LCS4 (Cupriavidus metallidurans (strain ATCC 43123 / DSM 2839 / NBRC 102507 / CH34)) Explore Q1LCS4 Go to UniProtKB: Q1LCS4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q1LCS4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TRS Query on TRS Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
FE2 Query on FE2 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [auth A]	B [auth A], C [auth A]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.72 Å
R-Value Free: 0.262 (Depositor), 0.260 (DCC)
R-Value Work: 0.192 (Depositor), 0.190 (DCC)
R-Value Observed: 0.196 (Depositor)

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.602	α = 90
b = 58.602	β = 90
c = 231.523	γ = 120

Software Package:

Software Name	Purpose
DENZO	data collection
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction
PHENIX	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2018-03-07

Deposition Author(s):

Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	CHE-1623856

Revision History (Full details and data files)

Version 1.0: 2018-03-07
Type: Initial release
Version 1.1: 2018-04-18
Changes: Data collection
Version 1.2: 2019-11-27
Changes: Author supporting evidence
Version 1.3: 2024-03-06
Changes: Data collection, Database references

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.