[English] 日本語
Yorodumi
- PDB-4n9m: Joint neutron/x-ray structure of urate oxidase in complex with 8-... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4n9m
TitleJoint neutron/x-ray structure of urate oxidase in complex with 8-hydroxyxanthine
ComponentsUricaseUrate oxidase
KeywordsOXIDOREDUCTASE / urate oxidase / uricase oxidoreductase
Function / homology
Function and homology information


urate oxidase activity / factor-independent urate hydroxylase / urate catabolic process / purine nucleobase metabolic process / peroxisome
Similarity search - Function
Urate Oxidase / Urate Oxidase; / Uricase, conserved site / Uricase signature. / Uricase / Uricase / Roll / Alpha Beta
Similarity search - Domain/homology
8-hydroxy-3,9-dihydro-1H-purine-2,6-dione / DEUTERATED WATER / Uricase
Similarity search - Component
Biological speciesAspergillus flavus (mold)
MethodNEUTRON DIFFRACTION / X-RAY DIFFRACTION / NUCLEAR REACTOR / Resolution: 2.023 Å
AuthorsOksanen, E. / Blakeley, M.P. / Budayova-Spano, M.
Citation
Journal: Plos One / Year: 2014
Title: The neutron structure of urate oxidase resolves a long-standing mechanistic conundrum and reveals unexpected changes in protonation.
Authors: Oksanen, E. / Blakeley, M.P. / El-Hajji, M. / Ryde, U. / Budayova-Spano, M.
#1: Journal: J R Soc Interface / Year: 2009
Title: Large crystal growth by thermal control allows combined X-ray and neutron crystallographic studies to elucidate the protonation states in Aspergillus flavus urate oxidase.
Authors: Oksanen, E. / Blakeley, M.P. / Bonnete, F. / Dauvergne, M.T. / Dauvergne, F. / Budayova-Spano, M.
History
DepositionOct 21, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2014Group: Database references
Revision 1.2Jun 13, 2018Group: Data collection / Database references / Refinement description
Category: citation / diffrn_detector ...citation / diffrn_detector / diffrn_radiation / diffrn_radiation_wavelength / diffrn_source / refine / refine_ls_shell / reflns / reflns_shell
Item: _citation.country / _citation.journal_id_ISSN ..._citation.country / _citation.journal_id_ISSN / _diffrn_detector.details / _diffrn_detector.pdbx_collection_date / _diffrn_detector.type / _diffrn_radiation.monochromator / _diffrn_radiation.pdbx_diffrn_protocol / _diffrn_radiation.pdbx_monochromatic_or_laue_m_l / _diffrn_radiation.pdbx_scattering_type / _diffrn_radiation_wavelength.wavelength / _diffrn_source.pdbx_wavelength / _diffrn_source.pdbx_wavelength_list / _diffrn_source.source / _refine.B_iso_max / _refine.B_iso_mean / _refine.B_iso_min / _refine.aniso_B[1][1] / _refine.aniso_B[2][2] / _refine.aniso_B[3][3] / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_d_res_high / _refine.ls_d_res_low / _refine.ls_number_reflns_R_free / _refine.ls_number_reflns_R_work / _refine.ls_number_reflns_obs / _refine.ls_percent_reflns_R_free / _refine.ls_percent_reflns_obs / _refine.overall_FOM_work_R_set / _refine.overall_SU_ML / _refine.pdbx_ls_sigma_F / _refine.pdbx_overall_phase_error / _refine.pdbx_refine_id / _refine.solvent_model_param_bsol / _refine.solvent_model_param_ksol / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _refine_ls_shell.d_res_high / _refine_ls_shell.d_res_low / _refine_ls_shell.number_reflns_R_free / _refine_ls_shell.number_reflns_R_work / _refine_ls_shell.number_reflns_all / _refine_ls_shell.pdbx_refine_id / _refine_ls_shell.pdbx_total_number_of_bins_used / _refine_ls_shell.percent_reflns_obs / _reflns.d_resolution_high / _reflns.d_resolution_low / _reflns.number_all / _reflns.number_obs / _reflns.pdbx_Rmerge_I_obs / _reflns.pdbx_netI_over_sigmaI / _reflns.percent_possible_obs / _reflns_shell.Rmerge_I_obs / _reflns_shell.d_res_high / _reflns_shell.d_res_low / _reflns_shell.meanI_over_sigI_obs / _reflns_shell.number_unique_all / _reflns_shell.percent_possible_all

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Uricase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4104
Polymers34,1841
Non-polymers2273
Water3,369187
1
A: Uricase
hetero molecules

A: Uricase
hetero molecules

A: Uricase
hetero molecules

A: Uricase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,64116
Polymers136,7344
Non-polymers90612
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_556-x,y,-z+11
crystal symmetry operation4_556x,-y,-z+11
Buried area24500 Å2
ΔGint-163 kcal/mol
Surface area42050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.180, 96.260, 105.510
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 / Urate oxidase


Mass: 34183.590 Da / Num. of mol.: 1
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-8HX / 8-hydroxy-3,9-dihydro-1H-purine-2,6-dione / 8-hydroxyxanthine / Uric acid


Mass: 168.110 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H4N4O3
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-DOD / water / Heavy water


Mass: 18.015 Da / Num. of mol.: 187 / Source method: isolated from a natural source / Formula: D2O

-
Experimental details

-
Experiment

Experiment
MethodNumber of used crystals
NEUTRON DIFFRACTION1
X-RAY DIFFRACTION1

-
Sample preparation

CrystalDensity Matthews: 2.98 Å3/Da / Density % sol: 58.67 %
Crystal growTemperature: 291 K / Method: temperature-controlled batch / pH: 8.5
Details: 5 % PEG 8000, 0.1 M NACL, 0.1 M TRISHCL PD 8.5, 8 MG/ML URATE OXIDASE, temperature-controlled batch, temperature 291K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12931
22931
Diffraction source
SourceTypeIDWavelength (Å)
SEALED TUBEOTHER11.54
NUCLEAR REACTOROTHER23.25-4.15
Detector
TypeIDDetectorDateDetails
MAR scanner 345 mm plate1IMAGE PLATEOct 28, 2008Xenocs
CUSTOM-MADE2IMAGE PLATEAug 30, 2008
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1multilayer mirrorSINGLE WAVELENGTHMx-ray1
2Ni/Ti multilayer filterLAUELneutron1
Radiation wavelength
IDWavelength (Å)Relative weight
11.541
23.251
34.151
Reflection

Entry-ID: 4N9M

Resolution (Å)Num. allNum. obs% possible obs (%)Rmerge(I) obsDiffraction-IDNet I/σ(I)
2-2098.50.04123.56
2.3-40.06131791317972.20.13327.9
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-IDNum. unique all% possible all
2-2.140.1459.541
2.3-2.420.192.22132850.6

-
Processing

Software
NameVersionClassification
LADI-IIIsoftwaredata collection
MOLREPphasing
PHENIX(phenix.refine: 1.7_650)refinement
LAUEGENdata reduction
SCALAdata scaling
Refinement

Baniso 12: 0 Å2 / Baniso 13: 0 Å2 / Baniso 23: -0 Å2 / Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Stereochemistry target values: ML / Solvent model: FLAT BULK SOLVENT MODEL

Resolution (Å)Refine-IDBiso max (Å2)Biso mean (Å2)Biso min (Å2)Baniso 11 (Å2)Baniso 22 (Å2)Baniso 33 (Å2)Rfactor RfreeRfactor RworkRfactor obsNum. reflection RfreeNum. reflection RworkNum. reflection obs% reflection Rfree (%)% reflection obs (%)FOM work R setSU MLDiffraction-IDσ(F)Phase errorBsol (Å2)ksol (e/Å3)
2.023-19.209X-RAY DIFFRACTION75.119.132.5915.74235.50131.36150.18870.16660.167813172502726344597.640.75730.2111.9919.4325.0070.365
2.298-40.067NEUTRON DIFFRACTION14.55847.90636.46840.28840.25860.2601663131745.0371.0820200.6
Refinement stepCycle: LAST / Resolution: 2.298→40.067 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2328 0 14 187 2529
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0755246
X-RAY DIFFRACTIONf_angle_d2.4098830
X-RAY DIFFRACTIONf_chiral_restr0.048374
X-RAY DIFFRACTIONf_plane_restr0.002738
X-RAY DIFFRACTIONf_dihedral_angle_d16.2751337
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-IDNum. reflection allTotal num. of bins used% reflection obs (%)
2.0231-2.1040.30581220.22862311X-RAY DIFFRACTION2433981
2.104-2.19960.19831450.1962775X-RAY DIFFRACTION29209100
2.1996-2.31540.22681490.19052807X-RAY DIFFRACTION29569100
2.3154-2.46020.24321480.18962821X-RAY DIFFRACTION29699100
2.4602-2.64970.2111490.1852831X-RAY DIFFRACTION29809100
2.6497-2.91550.21071490.18612842X-RAY DIFFRACTION29919100
2.9155-3.33550.1981500.17362833X-RAY DIFFRACTION29839100
3.3355-4.19510.16461510.14292864X-RAY DIFFRACTION30159100
4.1951-19.20970.13141540.13452943X-RAY DIFFRACTION3097998
2.3-2.47560.4472910.36221754NEUTRON DIFFRACTION1845551
2.4756-2.72470.317980.32691985NEUTRON DIFFRACTION2083557
2.7247-3.11880.36651300.29052370NEUTRON DIFFRACTION2500568
3.1188-3.92880.29011650.23252983NEUTRON DIFFRACTION3148585
3.9288-40.07320.20951790.21783419NEUTRON DIFFRACTION3598593

+
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