[English] 日本語
Yorodumi
- PDB-5ll1: Crystal structure of urate oxidase from zebrafish -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ll1
TitleCrystal structure of urate oxidase from zebrafish
ComponentsUricase
KeywordsOXIDOREDUCTASE / uric acid / urate / purine metabolism / uricolytic activities
Function / homology
Function and homology information


urate oxidase activity / factor-independent urate hydroxylase / purine nucleobase catabolic process / urate catabolic process / urate metabolic process / peroxisome / protein homotetramerization
Similarity search - Function
Urate Oxidase / Urate Oxidase; / Uricase / Uricase / Roll / Alpha Beta
Similarity search - Domain/homology
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsZanotti, G. / Cendron, l. / Percudani, R. / Berni, R.
CitationJournal: Sci Rep / Year: 2016
Title: Catalysis and Structure of Zebrafish Urate Oxidase Provide Insights into the Origin of Hyperuricemia in Hominoids.
Authors: Marchetti, M. / Liuzzi, A. / Fermi, B. / Corsini, R. / Folli, C. / Speranzini, V. / Gandolfi, F. / Bettati, S. / Ronda, L. / Cendron, L. / Berni, R. / Zanotti, G. / Percudani, R.
History
DepositionJul 26, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 25, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Uricase
B: Uricase
C: Uricase
D: Uricase
E: Uricase
F: Uricase
G: Uricase
H: Uricase


Theoretical massNumber of molelcules
Total (without water)273,9148
Polymers273,9148
Non-polymers00
Water1,56787
1
A: Uricase
B: Uricase
C: Uricase
D: Uricase


Theoretical massNumber of molelcules
Total (without water)136,9574
Polymers136,9574
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24630 Å2
ΔGint-151 kcal/mol
Surface area44670 Å2
MethodPISA
2
E: Uricase
F: Uricase
G: Uricase
H: Uricase


Theoretical massNumber of molelcules
Total (without water)136,9574
Polymers136,9574
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24530 Å2
ΔGint-143 kcal/mol
Surface area44720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.341, 127.415, 132.604
Angle α, β, γ (deg.)90.00, 102.21, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Uricase / Urate oxidase


Mass: 34239.238 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: uox / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q6DG85, factor-independent urate hydroxylase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / 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: 2.68 Å3/Da / Density % sol: 54 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8.5 / Details: Tris-HCl 0.1M, 8% PEG 8000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 5, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.8→83.3 Å / Num. obs: 64855 / % possible obs: 94.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.168 / Net I/σ(I): 5.2
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.427 / Mean I/σ(I) obs: 2.2 / % possible all: 89

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1R56

1r56


Resolution: 2.8→64.803 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.99
RfactorNum. reflection% reflectionSelection details
Rfree0.2575 3235 5 %Random selection
Rwork0.1967 ---
obs0.1997 64764 94.77 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.8→64.803 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18584 0 0 87 18671
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0119004
X-RAY DIFFRACTIONf_angle_d1.41225752
X-RAY DIFFRACTIONf_dihedral_angle_d14.4117040
X-RAY DIFFRACTIONf_chiral_restr0.0632920
X-RAY DIFFRACTIONf_plane_restr0.0073288
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.84180.37241130.26092528X-RAY DIFFRACTION89
2.8418-2.88630.30331130.24972527X-RAY DIFFRACTION89
2.8863-2.93360.32011240.24482509X-RAY DIFFRACTION90
2.9336-2.98420.33521380.25282483X-RAY DIFFRACTION90
2.9842-3.03840.31541460.23542570X-RAY DIFFRACTION91
3.0384-3.09690.31611280.24092556X-RAY DIFFRACTION91
3.0969-3.16010.31931620.23032550X-RAY DIFFRACTION91
3.1601-3.22880.27911320.23332609X-RAY DIFFRACTION93
3.2288-3.30390.27971370.23192611X-RAY DIFFRACTION93
3.3039-3.38650.30231370.23772638X-RAY DIFFRACTION93
3.3865-3.47810.27391470.21852636X-RAY DIFFRACTION94
3.4781-3.58040.27351150.22122707X-RAY DIFFRACTION95
3.5804-3.6960.32021540.27152672X-RAY DIFFRACTION96
3.696-3.8280.30331530.23862739X-RAY DIFFRACTION97
3.828-3.98130.27371320.21242707X-RAY DIFFRACTION97
3.9813-4.16240.26341490.17552799X-RAY DIFFRACTION99
4.1624-4.38190.17681550.14612798X-RAY DIFFRACTION99
4.3819-4.65630.21251530.13592793X-RAY DIFFRACTION99
4.6563-5.01570.18051550.12672809X-RAY DIFFRACTION99
5.0157-5.52020.18711550.1352797X-RAY DIFFRACTION99
5.5202-6.31840.20571480.15792813X-RAY DIFFRACTION99
6.3184-7.95830.24511580.16672838X-RAY DIFFRACTION99
7.9583-64.82020.19391310.16332840X-RAY DIFFRACTION97

+
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