[English] 日本語
Yorodumi
- PDB-4ynh: Structure of the C. elegans SAS-5 Implico dimerization domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ynh
TitleStructure of the C. elegans SAS-5 Implico dimerization domain
ComponentsSpindle assembly abnormal protein 5
KeywordsSTRUCTURAL PROTEIN / SAS-5 / Centriole / Dimerization domain
Function / homology: / Spindle assembly abnormal protein 5, implico domain / centriole assembly / centriole replication / centrosome duplication / centriole / cytoplasm / Spindle assembly abnormal protein 5
Function and homology information
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1 Å
AuthorsRogala, K.B. / Vakonakis, I. / Hatzopoulos, G.N.
CitationJournal: Elife / Year: 2015
Title: The Caenorhabditis elegans protein SAS-5 forms large oligomeric assemblies critical for centriole formation.
Authors: Rogala, K.B. / Dynes, N.J. / Hatzopoulos, G.N. / Yan, J. / Pong, S.K. / Robinson, C.V. / Deane, C.M. / Gonczy, P. / Vakonakis, I.
History
DepositionMar 10, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 10, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 26, 2015Group: Database references
Revision 1.2May 8, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Spindle assembly abnormal protein 5
B: Spindle assembly abnormal protein 5


Theoretical massNumber of molelcules
Total (without water)13,1452
Polymers13,1452
Non-polymers00
Water2,234124
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3060 Å2
ΔGint-18 kcal/mol
Surface area7360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)27.180, 36.290, 42.600
Angle α, β, γ (deg.)90.000, 97.500, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Spindle assembly abnormal protein 5 / SAS-5


Mass: 6572.445 Da / Num. of mol.: 2 / Fragment: dimerization domain, UNP residues 210-265
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: sas-5, F35B12.5 / Production host: Escherichia coli (E. coli) / References: UniProt: Q20010
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / 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: 1.58 Å3/Da / Density % sol: 22.38 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.1 M MES/imidazole pH 6.4, 10% w/v PEG 20,000, 20% v/v PEG MME 550, 0.1 M carboxylic acids mixture

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 31, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1→42.235 Å / Num. all: 44263 / Num. obs: 44263 / % possible obs: 99.4 % / Redundancy: 6.9 % / Biso Wilson estimate: 6.78 Å2 / Rpim(I) all: 0.044 / Rrim(I) all: 0.116 / Rsym value: 0.108 / Net I/av σ(I): 2.588 / Net I/σ(I): 12 / Num. measured all: 305514
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
1-1.056.80.7630.84332363640.3140.7634.298.3
1.05-1.126.90.4341.54159460170.1770.4346.298.7
1.12-1.26.90.272.43951957300.110.278.499.2
1.2-1.296.90.23.43715653650.0820.21099.5
1.29-1.416.90.1494.63396449050.0610.14911.699.9
1.41-1.586.90.1016.63118744930.0410.10114.7100
1.58-1.836.80.0946.72692639430.0390.09417.2100
1.83-2.246.70.078.82239733650.0290.0720.6100
2.24-3.167.20.068.91881626050.0240.0624.7100
3.16-18.4867.20.0945.11063214760.0380.09426.599.6

-
Processing

Software
NameVersionClassification
SCALA3.3.20data scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
RefinementResolution: 1→18.486 Å / SU ML: 0.08 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 12.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1491 2232 5.04 %
Rwork0.1281 42016 -
obs0.1291 44248 99.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 96.71 Å2 / Biso mean: 11.6337 Å2 / Biso min: 2.69 Å2
Refinement stepCycle: final / Resolution: 1→18.486 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms895 0 0 124 1019
Biso mean---23.53 -
Num. residues----116
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071035
X-RAY DIFFRACTIONf_angle_d1.1521420
X-RAY DIFFRACTIONf_chiral_restr0.057157
X-RAY DIFFRACTIONf_plane_restr0.006201
X-RAY DIFFRACTIONf_dihedral_angle_d12.549420
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1-1.02170.18041270.18172559268698
1.0217-1.04550.20851630.15812584274798
1.0455-1.07170.15641530.13372558271198
1.0717-1.10060.1331210.12562614273599
1.1006-1.1330.14211430.11582620276399
1.133-1.16960.13271390.10952595273499
1.1696-1.21140.13741150.10722627274299
1.2114-1.25990.12481370.098326282765100
1.2599-1.31720.11891330.101726332766100
1.3172-1.38660.12281450.102526322777100
1.3866-1.47340.1351450.108726302775100
1.4734-1.58710.13331540.109226262780100
1.5871-1.74680.14581330.121926612794100
1.7468-1.99930.14971440.136126512795100
1.9993-2.51780.14511300.139826842814100
2.5178-18.48880.1731500.145127142864100

+
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