[English] 日本語
Yorodumi
- PDB-3i2n: Crystal Structure of WD40 repeats protein WDR92 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3i2n
TitleCrystal Structure of WD40 repeats protein WDR92
ComponentsWD repeat-containing protein 92
KeywordsTRANSCRIPTION / WD40 repeats / WDR92 / Structural Genomics / Structural Genomics Consortium / SGC / Apoptosis / WD repeat
Function / homology
Function and homology information


ubiquitin binding / apoptotic process
Similarity search - Function
: / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily ...: / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta
Similarity search - Domain/homology
WD repeat-containing protein 92
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsAmaya, M.F. / Li, Z. / He, H. / Seitova, A. / Ni, S. / Edwards, A.M. / Arrowsmith, C.H. / Weigelt, J. / Bountra, C. / Bochkarev, A. ...Amaya, M.F. / Li, Z. / He, H. / Seitova, A. / Ni, S. / Edwards, A.M. / Arrowsmith, C.H. / Weigelt, J. / Bountra, C. / Bochkarev, A. / Min, J. / Ouyang, H. / Structural Genomics Consortium (SGC)
CitationJournal: Protein Cell / Year: 2011
Title: Structure and function of WD40 domain proteins.
Authors: Xu, C. / Min, J.
History
DepositionJun 29, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 18, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Apr 18, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: WD repeat-containing protein 92


Theoretical massNumber of molelcules
Total (without water)39,7921
Polymers39,7921
Non-polymers00
Water3,045169
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.052, 70.052, 84.656
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43

-
Components

#1: Protein WD repeat-containing protein 92 / WD repeat-containing protein Monad


Mass: 39792.402 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WDR92 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96MX6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / 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: 2.61 Å3/Da / Density % sol: 52.87 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.35M Na/K phosphate, pH7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E DW / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: May 22, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 29854 / % possible obs: 99.8 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.07 / Χ2: 1.77 / Net I/σ(I): 14.1
Reflection shell
Resolution (Å)Redundancy (%)Num. unique allΧ2% possible allRmerge(I) obs
1.95-2.024.429071.22398.4
2.02-2.16.929881.3611000.894
2.1-2.27.229981.481000.647
2.2-2.317.329521.5661000.503
2.31-2.467.429741.6411000.372
2.46-2.657.429881.6821000.25
2.65-2.917.530081.8421000.148
2.91-3.337.530032.1081000.078
3.33-4.27.629892.2941000.045
4.2-507.430472.16999.50.034

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→25.18 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.939 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 5.177 / SU ML: 0.145 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.178 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.264 1513 5.1 %RANDOM
Rwork0.226 ---
obs0.228 29819 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 95.33 Å2 / Biso mean: 45.705 Å2 / Biso min: 25.31 Å2
Baniso -1Baniso -2Baniso -3
1-1.22 Å20 Å20 Å2
2--1.22 Å20 Å2
3----2.44 Å2
Refinement stepCycle: LAST / Resolution: 1.95→25.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2556 0 0 169 2725
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0222615
X-RAY DIFFRACTIONr_angle_refined_deg1.7631.9413548
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5925344
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.56524.495109
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.54615398
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.8871513
X-RAY DIFFRACTIONr_chiral_restr0.1140.2392
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022000
X-RAY DIFFRACTIONr_nbd_refined0.2150.21194
X-RAY DIFFRACTIONr_nbtor_refined0.3090.21739
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1780.2205
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1850.237
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1950.29
X-RAY DIFFRACTIONr_mcbond_it1.1531.51751
X-RAY DIFFRACTIONr_mcangle_it1.84822698
X-RAY DIFFRACTIONr_scbond_it2.54831005
X-RAY DIFFRACTIONr_scangle_it3.7124.5850
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.415 114 -
Rwork0.342 2036 -
all-2150 -
obs--97.99 %

+
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://pdbjlc1.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