[English] 日本語
Yorodumi
- PDB-1ws3: Urate oxidase from aspergillus flavus complexed with uracil -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ws3
TitleUrate oxidase from aspergillus flavus complexed with uracil
ComponentsUricase
KeywordsOXIDOREDUCTASE / uric acid degradation / dimeric barrel / tunnel-shaped protein
Function / homology
Function and homology information


purine nucleobase catabolic process / factor-independent urate hydroxylase / urate oxidase activity / urate catabolic process / peroxisome
Similarity search - Function
Urate Oxidase / Urate Oxidase; / Uricase, conserved site / Uricase signature. / Uricase / Uricase / Roll / Alpha Beta
Similarity search - Domain/homology
Biological speciesAspergillus flavus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsRetailleau, P. / Colloc'h, N. / Vivares, D. / Bonnete, F. / Castro, B. / El Hajji, M. / Prange, T.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2005
Title: Urate oxidase from Aspergillus flavus: new crystal-packing contacts in relation to the content of the active site.
Authors: Retailleau, P. / Colloc'h, N. / Vivares, D. / Bonnete, F. / Castro, B. / El Hajji, M. / Prange, T.
#1: Journal: Nat.Struct.Biol. / Year: 1997
Title: Crystal structure of the protein drug urate oxidase-inhibitor complex at 2.05 A resolution
Authors: Colloc'h, N. / El Hajji, M. / Bachet, B. / L'Hermite, G. / Schiltz, M. / Castro, B. / Mornon, J.P.
History
DepositionOct 29, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 22, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 28, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.4Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Uricase
B: Uricase
C: Uricase
D: Uricase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,2478
Polymers136,7984
Non-polymers4484
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24440 Å2
ΔGint-94 kcal/mol
Surface area44960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.601, 140.601, 151.076
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Detailsthe biologically homotetrameric asembly corresponds to the asymmetric unit content

-
Components

#1: Protein
Uricase / urate oxidase


Mass: 34199.586 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus flavus (mold) / Production host: Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: Q00511, factor-independent urate hydroxylase
#2: Chemical
ChemComp-URA / URACIL


Mass: 112.087 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H4N2O2

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.24 Å3/Da / Density % sol: 61.72 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8
Details: pH 8.00, VAPOR DIFFUSION, SITTING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 291 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.972 / Wavelength: 0.972 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 9, 2003 / Details: CURVATED MIRRORS
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972 Å / Relative weight: 1
ReflectionResolution: 3.2→36 Å / Num. obs: 28902 / % possible obs: 99.8 % / Redundancy: 4.4 % / Rsym value: 0.093 / Net I/σ(I): 13.3

-
Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
BUSTER-TNTrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1R51

1r51


Resolution: 3.2→15 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2 2885 -RANDOM
Rwork0.146 ---
all0.152 28896 --
obs-28896 99.9 %-
Refinement stepCycle: LAST / Resolution: 3.2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9475 0 32 0 9507
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.011
X-RAY DIFFRACTIONt_angle_deg1.23
X-RAY DIFFRACTIONt_dihedral_angle_d19.5

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more