4XFP | pdb_00004xfp

Crystal Structure of Highly Active Mutant of Bacillus sp. TB-90 Urate Oxidase

PDB DOI: https://doi.org/10.2210/pdb4XFP/pdb

Classification: OXIDOREDUCTASE
Organism(s): Bacillus sp. TB-90
Expression System: Escherichia coli DH5[alpha]
Mutation(s): Yes

Deposited: 2014-12-28 Released: 2016-01-13
Deposition Author(s): Hibi, T., Hayashi, Y., Kawamura, A., Itoh, T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.66 Å
R-Value Free:
0.184 (Depositor), 0.185 (DCC)
R-Value Work:
0.156 (Depositor), 0.158 (DCC)
R-Value Observed:
0.157 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Glycine Substitution of Surface Proline 287 Involves Entropic Enhancement of Bacillus sp. TB-90 Uricase Activity

Hibi, T., Hayashi, Y., Kawamura, A., Itoh, T., Fukada, H., Kishimoto, T., Nishiya, Y.

To be published.

Macromolecule Content

Total Structure Weight: 145.89 kDa
Atom Count: 10,739
Modeled Residue Count: 1,176
Deposited Residue Count: 1,268
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Urate oxidase	A, B, C, D	317	Bacillus sp. TB-90	Mutation(s): 1 Gene Names: uao EC: 1.7.3.3 (PDB Primary Data), 4.1.1.97 (UniProt)
UniProt
Find proteins for Q45697 (Bacillus sp. (strain TB-90)) Explore Q45697 Go to UniProtKB: Q45697
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q45697
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AZA Query on AZA Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] SDF format, chain J [auth C] SDF format, chain M [auth D] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain J [auth C] MOL2 format, chain M [auth D] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain J [auth C] mmCIF format, chain M [auth D]	E [auth A], H [auth B], J [auth C], M [auth D]	8-AZAXANTHINE C₄ H₃ N₅ O₂ KVGVQTOQSNJTJI-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain M [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain M [auth D]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain L [auth D] MOL2 format, chain G [auth A] MOL2 format, chain L [auth D] mmCIF format, chain G [auth A] mmCIF format, chain L [auth D]	G [auth A], L [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G [auth A] Focus chain L [auth D] Interactions & Density Focus chain G [auth A] Focus chain L [auth D]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain I [auth B] SDF format, chain K [auth C] SDF format, chain N [auth D] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain K [auth C] MOL2 format, chain N [auth D] mmCIF format, chain F [auth A] mmCIF format, chain I [auth B] mmCIF format, chain K [auth C] mmCIF format, chain N [auth D]	F [auth A], I [auth B], K [auth C], N [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain N [auth D] Interactions & Density Focus chain F [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain N [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.66 Å
R-Value Free: 0.184 (Depositor), 0.185 (DCC)
R-Value Work: 0.156 (Depositor), 0.158 (DCC)
R-Value Observed: 0.157 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 134.135	α = 90
b = 145.195	β = 90
c = 71.141	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
SCALEPACK	data reduction
PHASER	phasing
PDB_EXTRACT	data extraction
HKL-2000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2016-01-13

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2016-01-13
Type: Initial release
Version 1.1: 2020-02-05
Changes: Data collection, Derived calculations
Version 1.2: 2023-11-08
Changes: Data collection, Database references, Refinement description

4XFP | pdb_00004xfp

Crystal Structure of Highly Active Mutant of Bacillus sp. TB-90 Urate Oxidase

Literature

Glycine Substitution of Surface Proline 287 Involves Entropic Enhancement of Bacillus sp. TB-90 Uricase Activity

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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