[English] 日本語
Yorodumi
- PDB-4puv: URATE OXIDASE DI-AZIDE complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4puv
TitleURATE OXIDASE DI-AZIDE complex
ComponentsUricase
KeywordsOXYGEN BINDING / INHIBITION / DEGRADATION MECHANISM / PEROXISOME / PURINE METABOLISM / HETEROTETRAMER / AZIDE / OXIDOREDUCTASE
Function / homology
Function and homology information


urate oxidase activity / factor-independent urate hydroxylase / purine nucleobase catabolic process / 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 / FOURIER SYNTHESIS / Resolution: 1.3 Å
AuthorsColloc'h, N. / Prange, T.
Citation
Journal: Acta Crystallogr.,Sect.F / Year: 2014
Title: Azide inhibition of urate oxidase.
Authors: Gabison, L. / Colloc'h, N. / Prange, T.
#1: Journal: Bmc Struct.Biol. / Year: 2008
Title: Structural Analysis of Urate Oxidase in Complex with its Natural Substrate Inhibited by Cyanide: Mechanistic Implications.
Authors: Gabison, L. / Prange, T. / Colloc'h, N. / Hajji, M.E. / Castro, B. / Chiadmi, M.
History
DepositionMar 14, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 24, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2016Group: Other
Revision 1.2Feb 28, 2018Group: Database references / Refinement description / Structure summary
Category: audit_author / citation_author / software
Item: _audit_author.name / _citation_author.name / _software.name
Revision 1.3Nov 8, 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 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Uricase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3335
Polymers34,1841
Non-polymers1494
Water4,306239
1
A: Uricase
hetero molecules

A: Uricase
hetero molecules

A: Uricase
hetero molecules

A: Uricase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,33120
Polymers136,7344
Non-polymers59616
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_656-x+1,y,-z+11
crystal symmetry operation4_566x,-y+1,-z+11
Buried area27000 Å2
ΔGint-162 kcal/mol
Surface area42620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.180, 94.920, 104.530
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

-
Components

#1: Protein Uricase / Urate oxidase


Mass: 34183.590 Da / Num. of mol.: 1 / Fragment: UNP residues 2-302
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus flavus (mold) / Gene: uaZ, uox / Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast)
References: UniProt: Q00511, factor-independent urate hydroxylase
#2: Chemical ChemComp-AZI / AZIDE ION


Mass: 42.020 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: N3
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 239 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.92 Å3/Da / Density % sol: 57.18 %
Crystal growTemperature: 291 K / Method: batch method / pH: 8.5
Details: MIXING TWO SOLUTIONS A & B: SOLUTION A: PROTEIN (20 MG/ML) TRIS ACETATE BUFFER 0.05 M PH=8.5. SOLUTION B: TRIS ACETATE BUFFER 0.05 M + SODIUM AZIDE 0.3M. CRYSTALS HARVESTED 2 MONTHS AFTER ...Details: MIXING TWO SOLUTIONS A & B: SOLUTION A: PROTEIN (20 MG/ML) TRIS ACETATE BUFFER 0.05 M PH=8.5. SOLUTION B: TRIS ACETATE BUFFER 0.05 M + SODIUM AZIDE 0.3M. CRYSTALS HARVESTED 2 MONTHS AFTER CRYSTALLIZATION (AGED CRYSTALS), BATCH METHOD, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.938 / Wavelength: 0.938 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 21, 2014 / Details: BENT MIRROR
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.938 Å / Relative weight: 1
ReflectionResolution: 1.3→20 Å / Num. all: 97678 / Num. obs: 66686 / % possible obs: 98.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 4 / Redundancy: 4.7 % / Rmerge(I) obs: 0.072
Reflection shellResolution: 1.3→1.34 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.217 / % possible all: 99

-
Processing

Software
NameClassification
MxCuBEdata collection
SHELXmodel building
SHELXL-97refinement
XDSdata reduction
SCALAdata scaling
TRUNCATEdata scaling
SHELXDEphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4OQC

4oqc


Resolution: 1.3→20 Å / Num. parameters: 10481 / Num. restraintsaints: 9811 / σ(F): 4
StereochEM target val spec case: HYDROGENS KEPT AT THEIR THEORETICAL PLACES OTHER REFINEMENT REMARKS: ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28(1995)53-56
Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflection
Rwork0.1762 --
all0.2108 97678 -
obs0.1762 66686 98.8 %
Refine analyzeNum. disordered residues: 6 / Occupancy sum hydrogen: 2261.5 / Occupancy sum non hydrogen: 2603
Refinement stepCycle: LAST / Resolution: 1.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2362 0 10 239 2611
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.03
X-RAY DIFFRACTIONs_angle_d0.075
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes0.0291
X-RAY DIFFRACTIONs_zero_chiral_vol0.069
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.073
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.071
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.06
X-RAY DIFFRACTIONs_approx_iso_adps

+
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://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