[English] 日本語
Yorodumi
- PDB-4i99: Crystal structure of the SmcHead bound to the C-winged helix doma... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4i99
TitleCrystal structure of the SmcHead bound to the C-winged helix domain of ScpA
Components
  • Chromosome partition protein Smc
  • Putative uncharacterized protein
KeywordsDNA BINDING PROTEIN / winged-helix domain and SMC head domain / chromosome condensation / ScpB
Function / homology
Function and homology information


cohesin loader activity / chromosome condensation / mitotic sister chromatid cohesion / chromosome segregation / chromosome / double-stranded DNA binding / DNA replication / ATP hydrolysis activity / ATP binding / cytoplasm
Similarity search - Function
Structural maintenance of chromosome 1. Chain E / Segregation and condensation protein A / Segregation and condensation protein ScpA / Structural maintenance of chromosomes protein, prokaryotic / ScpA-like, C-terminal / Structural maintenance of chromosomes protein / SMCs flexible hinge / SMCs flexible hinge superfamily / SMC proteins Flexible Hinge Domain / SMC proteins Flexible Hinge Domain ...Structural maintenance of chromosome 1. Chain E / Segregation and condensation protein A / Segregation and condensation protein ScpA / Structural maintenance of chromosomes protein, prokaryotic / ScpA-like, C-terminal / 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 / Arc Repressor Mutant, subunit A / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Chromosome partition protein Smc / Segregation/condensation protein A
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsShin, H.C. / Soh, Y.M. / Oh, B.H.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2013
Title: An asymmetric SMC-kleisin bridge in prokaryotic condensin.
Authors: Burmann, F. / Shin, H.C. / Basquin, J. / Soh, Y.M. / Gimenez-Oya, V. / Kim, Y.G. / Oh, B.H. / Gruber, S.
History
DepositionDec 5, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 30, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 10, 2014Group: Database references
Revision 1.2Aug 23, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Chromosome partition protein Smc
B: Chromosome partition protein Smc
C: Putative uncharacterized protein
D: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,8107
Polymers100,5254
Non-polymers2853
Water1,63991
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7800 Å2
ΔGint-76 kcal/mol
Surface area32590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.855, 117.855, 94.482
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

-
Components

#1: Protein Chromosome partition protein Smc


Mass: 39856.270 Da / Num. of mol.: 2 / Fragment: Head domain, UNP RESIDUES 2-182, 1006-1172
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Strain: DSM 3638 / Gene: PF1843, smc / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): B834 (DE3) / References: UniProt: Q8TZY2
#2: Protein Putative uncharacterized protein / Segregation and condensation protein A


Mass: 10406.189 Da / Num. of mol.: 2 / Fragment: C-WHD, UNP RESIDUES126-212
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Strain: DSM 3638 / Gene: PF1842 / Plasmid: pProEx HTa / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) RIPL / References: UniProt: Q8TZY3
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE RESIDUES 183-1005 IN CHAIN A/B ARE DELETIONS

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.26 Å3/Da / Density % sol: 62.31 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 100mM Bicine, 220mM ammonium phosphate dibasic, 16% polyethylene glycol 3350, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 0.97932 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: Apr 18, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97932 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 57452 / % possible obs: 99.9 % / Redundancy: 10.4 % / Biso Wilson estimate: 30.7 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 31.84
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.363 / Mean I/σ(I) obs: 3.54 / % possible all: 99.8

-
Processing

Software
NameClassification
HKL-2000data collection
SHARPphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.3→29.46 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.236 5469 5 %random
Rwork0.221 ---
obs-57452 99.2 %-
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.41 Å0.41 Å
Refinement stepCycle: LAST / Resolution: 2.3→29.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6130 0 15 91 6236
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_improper_angle_d0.76
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.011
RfactorNum. reflection% reflection
Rfree0.335 928 -
Rwork0.326 --
obs-17532 98 %

+
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