5FRC

Structure of urate oxidase prepared by the 'soak-and-freeze' method under 42 bar of oxygen pressure

PDB DOI: https://doi.org/10.2210/pdb5FRC/pdb

Classification: OXIDOREDUCTASE
Organism(s): Aspergillus flavus
Expression System: Saccharomyces cerevisiae
Mutation(s): Yes

Deposited: 2015-12-16 Released: 2016-10-26
Deposition Author(s): Lafumat, B., Mueller-Dieckmann, C., Colloc'h, N., Prange, T., Royant, A., van der Linden, P., Carpentier, P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.44 Å
R-Value Free: 0.165
R-Value Work: 0.141
R-Value Observed: 0.143

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Gas-Sensitive Biological Crystals Processed in Pressurized Oxygen and Krypton Atmospheres: Deciphering Gas Channels in Proteins Using a Novel `Soak-and-Freeze' Methodology.

Lafumat, B., Mueller-Dieckmann, C., Colloc'h, N., Prange, T., Royant, A., van der Linden, P., Carpentier, P.

(2016) J Appl Crystallogr 49: 1478

DOI: https://doi.org/10.1107/S1600576716010992

Macromolecule Content

Total Structure Weight: 34.39 kDa
Atom Count: 2,841
Modelled Residue Count: 296
Deposited Residue Count: 302
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
URICASE	A	302	Aspergillus flavus	Mutation(s): 1 EC: 1.7.3.3
UniProt
Find proteins for Q00511 (Aspergillus flavus) Explore Q00511 Go to UniProtKB: Q00511
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q00511
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 B [auth A] MOL2 format, chain B [auth A]	B [auth A]	8-AZAXANTHINE C₄ H₃ N₅ O₂ KVGVQTOQSNJTJI-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
OXY Query on OXY Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A]	D [auth A]	OXYGEN MOLECULE O₂ MYMOFIZGZYHOMD-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.44 Å
R-Value Free: 0.165
R-Value Work: 0.141
R-Value Observed: 0.143
Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.898	α = 90
b = 95.351	β = 90
c = 104.672	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2016-10-26

Deposition Author(s):

Lafumat, B.

Mueller-Dieckmann, C.

Revision History (Full details and data files)

Version 1.0: 2016-10-26
Type: Initial release
Version 1.1: 2016-11-16
Changes: Structure summary
Version 1.2: 2018-02-21
Changes: Database references, Structure summary
Version 1.3: 2018-06-27
Changes: Data collection, Database references
Version 1.4: 2024-01-10
Changes: Data collection, Database references, Derived calculations, Other, Refinement description

Prepare Data

Validate Data

Deposit Data

Help and Resources

5FRC

Structure of urate oxidase prepared by the 'soak-and-freeze' method under 42 bar of oxygen pressure

Gas-Sensitive Biological Crystals Processed in Pressurized Oxygen and Krypton Atmospheres: Deciphering Gas Channels in Proteins Using a Novel `Soak-and-Freeze' Methodology.

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)