5Y2P

Crystal Structure of Bacillus sp. TB-90 Urate Oxidase Improved by Humidity Control at 89% RH

PDB DOI: https://doi.org/10.2210/pdb5Y2P/pdb

Classification: OXIDOREDUCTASE
Organism(s): Bacillus sp. TB-90
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2017-07-26 Released: 2018-08-08
Deposition Author(s): Itoh, T., Nishiya, Y.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.177
R-Value Work: 0.157
R-Value Observed: 0.158

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

Conformational Flexibility of Plastic Interface Loop Allows Entropic Adaptation of Urate Oxidase to Environmental pH.

Hibi, T., Itoh, T., Fukada, H., Kishimoto, T., Nishiya, Y.

To be published.

Macromolecule Content

Total Structure Weight: 72.31 kDa
Atom Count: 5,701
Modelled Residue Count: 607
Deposited Residue Count: 624
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uric acid degradation bifunctional protein	A, B	312	Bacillus sp. TB-90	Mutation(s): 0 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q45697
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AZA Query on AZA Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain H [auth B] MOL2 format, chain C [auth A] MOL2 format, chain H [auth B] mmCIF format, chain C [auth A] mmCIF format, chain H [auth B]	C [auth A], H [auth B]	8-AZAXANTHINE C₄ H₃ N₅ O₂ KVGVQTOQSNJTJI-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain H [auth B] Interactions & Density Focus chain C [auth A] Focus chain H [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B]	F [auth A] G [auth A] K [auth B] L [auth B] M [auth B] F [auth A], G [auth A], K [auth B], L [auth B], M [auth B], N [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B]
K Query on K Download Ideal Coordinates CCD File SDF format, chain J [auth B] MOL2 format, chain J [auth B] mmCIF format, chain J [auth B]	J [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain J [auth B] Interactions & Density Focus chain J [auth B]
OXY Query on OXY Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain I [auth B] MOL2 format, chain D [auth A] MOL2 format, chain I [auth B] mmCIF format, chain D [auth A] mmCIF format, chain I [auth B]	D [auth A], I [auth B]	OXYGEN MOLECULE O₂ MYMOFIZGZYHOMD-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain I [auth B] Interactions & Density Focus chain D [auth A] Focus chain I [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
OCS Query on OCS	A, B	L-PEPTIDE LINKING	C₃ H₇ N O₅ S		CYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.177
R-Value Work: 0.157
R-Value Observed: 0.158
Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.095	α = 90
b = 133.885	β = 90
c = 145.797	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2018-08-08

Deposition Author(s):

Itoh, T.

Nishiya, Y.

Revision History (Full details and data files)

Version 1.0: 2018-08-08
Type: Initial release
Version 1.1: 2020-09-02
Changes: Derived calculations, Structure summary
Version 1.2: 2023-11-22
Changes: Data collection, Database references, Refinement description

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Help and Resources

5Y2P

Crystal Structure of Bacillus sp. TB-90 Urate Oxidase Improved by Humidity Control at 89% RH

Conformational Flexibility of Plastic Interface Loop Allows Entropic Adaptation of Urate Oxidase to Environmental pH.

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)