[English] 日本語
Yorodumi
- PDB-2yzb: Crystal structure of uricase from Arthrobacter globiformis in com... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2yzb
TitleCrystal structure of uricase from Arthrobacter globiformis in complex with uric acid (substrate)
ComponentsUricase
KeywordsOXIDOREDUCTASE / uricase / uric acid
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 speciesArthrobacter globiformis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsJuan, E.C.M. / Hossain, M.T. / Hoque, M.M. / Suzuki, K. / Sekiguchi, T. / Takenaka, A.
CitationJournal: To be Published
Title: Trapping of the uric acid substrate in the crystal structure of urate oxidase from Arthrobacter globiformis
Authors: Juan, E.C.M. / Hossain, M.T. / Hoque, M.M. / Yamamoto, T. / Imamura, S. / Suzuki, K. / Sekiguchi, T. / Takenaka, A.
History
DepositionMay 5, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 6, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
E: Uricase
F: Uricase
G: Uricase
H: Uricase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)272,55016
Polymers271,2058
Non-polymers1,3458
Water24,5181361
1
A: Uricase
B: Uricase
C: Uricase
D: Uricase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,2758
Polymers135,6034
Non-polymers6724
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25170 Å2
ΔGint-97 kcal/mol
Surface area39480 Å2
MethodPISA
2
E: Uricase
F: Uricase
G: Uricase
H: Uricase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,2758
Polymers135,6034
Non-polymers6724
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25050 Å2
ΔGint-98 kcal/mol
Surface area39640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.480, 123.240, 284.550
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
Uricase


Mass: 33900.629 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Arthrobacter globiformis (bacteria)
References: UniProt: D0VWQ1*PLUS, factor-independent urate hydroxylase
#2: Chemical
ChemComp-URC / URIC ACID / 7,9-DIHYDRO-1H-PURINE-2,6,8(3H)-TRIONE


Mass: 168.110 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C5H4N4O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1361 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE DATABASE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST IN UNP. IT WILL BE SUBMITTED TO UNP ...THE SEQUENCE DATABASE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST IN UNP. IT WILL BE SUBMITTED TO UNP DATABASE SOON.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.73 Å3/Da / Density % sol: 54.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: PEG 8000, lithium sulfate, sodium borate buffer, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 3, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 213158 / % possible obs: 90.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Rmerge(I) obs: 0.09
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.341 / % possible all: 73.5

-
Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1uox

1uox
PDB Unreleased entry


Resolution: 1.9→20 Å / Cross valid method: THROUGHOUT / σ(F): 3
RfactorNum. reflection% reflectionSelection details
Rfree0.2226 18353 -Random
Rwork0.19 ---
all-233408 --
obs-184396 79 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--20.668 Å20 Å20 Å2
2--4.311 Å20 Å2
3---16.357 Å2
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18277 0 96 1361 19734

+
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