[English] 日本語
Yorodumi
- PDB-4r8x: Crystal structure of a uricase from Bacillus fastidious -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4r8x
TitleCrystal structure of a uricase from Bacillus fastidious
ComponentsUricase
KeywordsHYDROLASE / Bacillus fastidious uricase / fold / stability
Function / homology
Function and homology information


urate oxidase activity / factor-independent urate hydroxylase / purine nucleobase catabolic process / urate catabolic process
Similarity search - Function
Urate Oxidase / Urate Oxidase; / Uricase / Uricase / Roll / Alpha Beta
Similarity search - Domain/homology
factor independent urate hydroxylase
Similarity search - Component
Biological speciesBacillus fastidiosus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.401 Å
AuthorsFeng, J. / Wang, L. / Liu, H.B. / Liu, L. / Liao, F.
CitationJournal: Appl.Microbiol.Biotechnol. / Year: 2015
Title: Crystal structure of Bacillus fastidious uricase reveals an unexpected folding of the C-terminus residues crucial for thermostability under physiological conditions.
Authors: Feng, J. / Wang, L. / Liu, H. / Yang, X. / Liu, L. / Xie, Y. / Liu, M. / Zhao, Y. / Li, X. / Wang, D. / Zhan, C.G. / Liao, F.
History
DepositionSep 3, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 27, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Database references
Category: citation / citation_author ...citation / citation_author / database_2 / struct_ref_seq_dif
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.2Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)143,4394
Polymers143,4394
Non-polymers00
Water34,5171916
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22560 Å2
ΔGint-103 kcal/mol
Surface area47360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.152, 77.473, 77.295
Angle α, β, γ (deg.)68.65, 65.01, 90.32
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein
Uricase


Mass: 35859.809 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus fastidiosus (bacteria) / Production host: Escherichia coli (E. coli)
References: UniProt: C5HDG5, 3-hydroxyisobutyryl-CoA hydrolase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1916 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 50.05 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Tris, 20% PEG 3350, 0.2M sodium citrate, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 10, 2012
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. all: 269102 / Num. obs: 256186 / % possible obs: 95.2 % / Biso Wilson estimate: 14.12 Å2
Reflection shellResolution: 1.4→1.45 Å / % possible all: 93.1

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASESphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1J2G

1j2g


Resolution: 1.401→32.039 Å / FOM work R set: 0.8645 / SU ML: 0.15 / σ(F): 1.96 / Phase error: 21.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2068 12864 5.02 %Random
Rwork0.1722 ---
all0.1739 269102 --
obs0.1739 256138 95.11 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 72.08 Å2 / Biso mean: 19.22 Å2 / Biso min: 9.18 Å2
Refinement stepCycle: LAST / Resolution: 1.401→32.039 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9905 0 0 1916 11821
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00610190
X-RAY DIFFRACTIONf_angle_d1.08113842
X-RAY DIFFRACTIONf_chiral_restr0.0751543
X-RAY DIFFRACTIONf_plane_restr0.0051811
X-RAY DIFFRACTIONf_dihedral_angle_d12.5713642
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4005-1.41640.28354430.22437663810690
1.4164-1.43310.25724030.20847962836593
1.4331-1.45060.26194360.20297932836893
1.4506-1.46890.25054190.19777908832793
1.4689-1.48820.26394550.19348018847393
1.4882-1.50860.24434130.19278002841594
1.5086-1.53020.25364200.17987905832594
1.5302-1.5530.21544580.16538011846994
1.553-1.57730.22944330.16288004843794
1.5773-1.60320.22124090.16277988839794
1.6032-1.63080.22664020.16088096849894
1.6308-1.66040.20354160.15868053846994
1.6604-1.69240.23524460.16728097854395
1.6924-1.72690.23094240.16228066849095
1.7269-1.76450.21343970.15928124852195
1.7645-1.80550.21284080.16138165857395
1.8055-1.85070.22794390.16348122856195
1.8507-1.90070.20714280.16038185861396
1.9007-1.95660.20583860.168167855396
1.9566-2.01980.20314350.16248220865596
2.0198-2.09190.19624280.15868267869596
2.0919-2.17570.20484320.16528136856896
2.1757-2.27470.19884380.1698306874497
2.2747-2.39460.21824400.18238168860897
2.3946-2.54450.22814640.19128252871697
2.5445-2.74090.22954660.19888256872297
2.7409-3.01650.20714240.18598271869597
3.0165-3.45260.18994170.17318272868997
3.4526-4.34820.17374310.15398437886899
4.3482-32.04760.17634540.17148221867596

+
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