[English] 日本語
Yorodumi
- PDB-6ivh: Crystal structure of the N-terminal domain of ScpA derived from T... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ivh
TitleCrystal structure of the N-terminal domain of ScpA derived from Thermococcus onnurineus
ComponentsSegregation and condensation protein A
KeywordsCELL CYCLE / CYTOSOLIC PROTEIN / Condensin / kleisin
Function / homologySegregation and condensation protein A / Segregation and condensation protein ScpA / ScpA-like, C-terminal / cell cycle / Uncharacterized protein
Function and homology information
Biological speciesThermococcus onnurineus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsJeon, J.-H. / Shin, H.-C. / Oh, B.-H.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (Korea)NRF-2018R1A2B3004764 Korea, Republic Of
CitationJournal: Iucrj / Year: 2020
Title: Archaeal Smc-based condensin lacking kite subunits
Authors: Jeon, J.-H. / Lee, H.-S. / Shin, H.-C. / Kwak, M.-J. / Kim, Y.-K. / Gruber, S. / Oh, B.-H.
History
DepositionDec 4, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 22, 2020Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Segregation and condensation protein A


Theoretical massNumber of molelcules
Total (without water)15,1621
Polymers15,1621
Non-polymers00
Water181
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6110 Å2
Unit cell
Length a, b, c (Å)76.984, 76.984, 39.934
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

-
Components

#1: Protein Segregation and condensation protein A


Mass: 15161.518 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus onnurineus (strain NA1) (archaea)
Strain: NA1 / Gene: TON_1071 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B6YWU6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 2.25 Å3/Da / Density % sol: 45.41 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: crystal growth at 3.5 M sodium formate and 0.1 M sodium malonate, dehydration for 2 h in the reservoir solution containing additional 10% glycerol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 25, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 8911 / % possible obs: 97.2 % / Redundancy: 6.7 % / Biso Wilson estimate: 40.12 Å2 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.028 / Rrim(I) all: 0.084 / Χ2: 2.338 / Net I/σ(I): 15.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.5-2.5430.2794120.3270.1590.3240.93489.6
2.54-2.593.30.2783940.3170.1620.3250.92591.2
2.59-2.643.40.2794520.4030.1570.3230.88992.6
2.64-2.6940.2494080.7630.1220.281.17392.7
2.69-2.754.20.2754310.6670.1360.3091.23194.3
2.75-2.824.50.244370.8460.1140.2681.23896.5
2.82-2.894.70.2274510.8260.1060.2521.12994.9
2.89-2.964.90.2164440.8780.0990.2391.23197.4
2.96-3.055.80.1964610.9280.0840.2141.26299.1
3.05-3.156.10.1714420.9610.070.1861.44299.8
3.15-3.266.80.1384520.9840.0540.1481.68198.7
3.26-3.397.30.1174640.9850.0440.1251.799.4
3.39-3.558.20.0994560.9910.0360.1062.161100
3.55-3.738.50.0974350.9920.0340.1032.19199.8
3.73-3.978.90.0874870.9960.030.0922.85899.8
3.97-4.279.40.0744530.9970.0250.0783.33599.8
4.27-4.79.60.0664400.9970.0220.073.30199.8
4.7-5.389.80.0644740.9980.0210.0673.22100
5.38-6.789.50.0694580.9970.0230.0733.054100
6.78-5010.80.0544600.9990.0170.0563.62899.6

-
Phasing

PhasingMethod: SAD

-
Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RESOLVEmodel building
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: SAD / Resolution: 2.5→38.492 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.75 / Phase error: 25.14
Details: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS
RfactorNum. reflection% reflection
Rfree0.2589 882 9.91 %
Rwork0.2391 --
obs0.2416 8904 97.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 99.83 Å2 / Biso mean: 53.5061 Å2 / Biso min: 24.4 Å2
Refinement stepCycle: final / Resolution: 2.5→38.492 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms768 0 0 1 769
Biso mean---37.29 -
Num. residues----94
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004776
X-RAY DIFFRACTIONf_angle_d0.7321047
X-RAY DIFFRACTIONf_chiral_restr0.046126
X-RAY DIFFRACTIONf_plane_restr0.002131
X-RAY DIFFRACTIONf_dihedral_angle_d19.185489
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5001-2.65670.34411280.3081256138491
2.6567-2.86170.33221490.27681302145195
2.8617-3.14960.28561390.26531357149698
3.1496-3.60510.30181550.23481377153299
3.6051-4.54080.23031620.20513631525100
4.5408-38.49650.211490.231713671516100

+
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