[English] 日本語
Yorodumi
- PDB-5xei: Crystal structure of the Smc head domain with a coiled coil and j... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5xei
TitleCrystal structure of the Smc head domain with a coiled coil and joint derived from Pyrococcus yayanosii
ComponentsChromosome partition protein Smc
KeywordsDNA BINDING PROTEIN / CELL CYCLE / Condensin / Smc / head domain / ABC-ATPase
Function / homology
Function and homology information


chromosome condensation / sister chromatid cohesion / chromosome / DNA replication / ATP hydrolysis activity / DNA binding / ATP binding / cytoplasm
Similarity search - Function
Structural maintenance of chromosomes protein, prokaryotic / Structural maintenance of chromosomes protein / SMCs flexible hinge / SMCs flexible hinge superfamily / SMC proteins Flexible Hinge Domain / SMC proteins Flexible Hinge Domain / RecF/RecN/SMC, N-terminal / RecF/RecN/SMC N terminal domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Chromosome partition protein Smc
Similarity search - Component
Biological speciesPyrococcus yayanosii
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.599 Å
AuthorsLee, H. / Noh, H. / Oh, B.-H.
CitationJournal: Mol. Cell / Year: 2017
Title: Structure of Full-Length SMC and Rearrangements Required for Chromosome Organization
Authors: Diebold-Durand, M.L. / Lee, H. / Ruiz Avila, L.B. / Noh, H. / Shin, H.C. / Im, H. / Bock, F.P. / Burmann, F. / Durand, A. / Basfeld, A. / Ham, S. / Basquin, J. / Oh, B.-H. / Gruber, S.
History
DepositionApr 5, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 7, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Aug 30, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.3Nov 22, 2023Group: 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Chromosome partition protein Smc


Theoretical massNumber of molelcules
Total (without water)60,8251
Polymers60,8251
Non-polymers00
Water23413
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area27620 Å2
Unit cell
Length a, b, c (Å)120.320, 50.836, 122.057
Angle α, β, γ (deg.)90.000, 118.090, 90.000
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Chromosome partition protein Smc


Mass: 60825.113 Da / Num. of mol.: 1 / Fragment: UNP residues 1-254 and 907-1177
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus yayanosii (strain CH1 / JCM 16557) (archaea)
Strain: CH1 / JCM 16557 / Gene: smc, PYCH_01200 / Production host: Escherichia coli (E. coli) / References: UniProt: F8AFS8
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 2.83 Å3/Da / Density % sol: 56.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 7% PEG 3350, 4% Tacsimate pH4.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.97941 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 9, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97941 Å / Relative weight: 1
ReflectionResolution: 2.599→50 Å / Num. obs: 18871 / % possible obs: 92.8 % / Redundancy: 4.2 % / Biso Wilson estimate: 50.93 Å2 / Net I/σ(I): 13.7

-
Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data collection
HKL-2000data scaling
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
PHENIXphasing
HKLdata reduction
HKLdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XNS

5xns


Resolution: 2.599→39.625 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.43 / Phase error: 29.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2784 1903 10.08 %
Rwork0.2075 16968 -
obs0.2145 18871 92.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 149.22 Å2 / Biso mean: 64.9606 Å2 / Biso min: 29.48 Å2
Refinement stepCycle: final / Resolution: 2.599→39.625 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4087 0 0 13 4100
Biso mean---49.81 -
Num. residues----517
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014136
X-RAY DIFFRACTIONf_angle_d1.1815539
X-RAY DIFFRACTIONf_chiral_restr0.056622
X-RAY DIFFRACTIONf_plane_restr0.007719
X-RAY DIFFRACTIONf_dihedral_angle_d21.1652611
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5994-2.66440.3532930.313888898170
2.6644-2.73640.40341220.30131053117581
2.7364-2.81690.3391310.30271165129689
2.8169-2.90780.32631320.28731141127389
2.9078-3.01170.33421280.26171166129490
3.0117-3.13220.31931360.24941183131991
3.1322-3.27470.30621390.23221234137395
3.2747-3.44730.30281370.21471278141598
3.4473-3.66310.27151460.20611283142998
3.6631-3.94570.28651440.19781284142899
3.9457-4.34230.29571510.18771305145699
4.3423-4.96960.21391440.159413051449100
4.9696-6.25720.2731460.19681323146999
6.2572-39.62960.22761540.17941360151499

+
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