[English] 日本語
Yorodumi
- PDB-7duv: Structure of Sulfolobus solfataricus SegB protein -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7duv
TitleStructure of Sulfolobus solfataricus SegB protein
ComponentsSegB
KeywordsDNA BINDING PROTEIN
Function / homologyUncharacterized protein
Function and homology information
Biological speciesSaccharolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.2 Å
AuthorsYen, C.Y. / Lin, M.G. / Sun, Y.J. / Hsiao, C.D.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, Taiwan) Taiwan
CitationJournal: Nucleic Acids Res. / Year: 2021
Title: Chromosome segregation in Archaea: SegA- and SegB-DNA complex structures provide insights into segrosome assembly.
Authors: Yen, C.Y. / Lin, M.G. / Chen, B.W. / Ng, I.W. / Read, N. / Kabli, A.F. / Wu, C.T. / Shen, Y.Y. / Chen, C.H. / Barilla, D. / Sun, Y.J. / Hsiao, C.D.
History
DepositionJan 11, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 22, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2May 29, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: SegB
B: SegB
C: SegB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6405
Polymers41,4483
Non-polymers1922
Water1,00956
1
A: SegB

A: SegB


Theoretical massNumber of molelcules
Total (without water)27,6322
Polymers27,6322
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area4610 Å2
ΔGint-51 kcal/mol
Surface area9200 Å2
MethodPISA
2
B: SegB
C: SegB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8244
Polymers27,6322
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5370 Å2
ΔGint-83 kcal/mol
Surface area9040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.773, 61.773, 171.925
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and ((resid 37 through 38 and (name N...
21(chain B and ((resid 37 through 38 and (name N...
31(chain C and ((resid 37 through 38 and (name N...

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU

Dom-IDComponent-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYS(chain A and ((resid 37 through 38 and (name N...AA37 - 3837 - 38
12LYSLYS(chain A and ((resid 37 through 38 and (name N...AA35 - 10835 - 108
13LYSLYS(chain A and ((resid 37 through 38 and (name N...AA35 - 10835 - 108
14LYSLYS(chain A and ((resid 37 through 38 and (name N...AA35 - 10835 - 108
15LYSLYS(chain A and ((resid 37 through 38 and (name N...AA35 - 10835 - 108
21LYSLYS(chain B and ((resid 37 through 38 and (name N...BB37 - 3837 - 38
22LYSLYS(chain B and ((resid 37 through 38 and (name N...BB35 - 10835 - 108
23LYSLYS(chain B and ((resid 37 through 38 and (name N...BB35 - 10835 - 108
24LYSLYS(chain B and ((resid 37 through 38 and (name N...BB35 - 10835 - 108
25LYSLYS(chain B and ((resid 37 through 38 and (name N...BB35 - 10835 - 108
31LYSLYS(chain C and ((resid 37 through 38 and (name N...CC37 - 3837 - 38
32ARGARG(chain C and ((resid 37 through 38 and (name N...CC35 - 10635 - 106
33ARGARG(chain C and ((resid 37 through 38 and (name N...CC35 - 10635 - 106
34ARGARG(chain C and ((resid 37 through 38 and (name N...CC35 - 10635 - 106

-
Components

#1: Protein SegB


Mass: 13815.950 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2) (archaea)
Strain: ATCC 35092 / DSM 1617 / JCM 11322 / P2 / Gene: SSO0035 / Production host: Escherichia coli (E. coli) / References: UniProt: Q981B2
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 56 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 41.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: ammonium sulfate, PEG 4000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 0.993 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Feb 28, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.993 Å / Relative weight: 1
ReflectionResolution: 3.2→30 Å / Num. obs: 5959 / % possible obs: 99.1 % / Redundancy: 12.2 % / Rmerge(I) obs: 0.158 / Rpim(I) all: 0.046 / Rrim(I) all: 0.164 / Χ2: 1.063 / Net I/σ(I): 6.4 / Num. measured all: 72822
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.2-3.3110.51.125460.9620.3331.1711.00396.5
3.31-3.4511.50.875870.9540.2540.9081.10898.5
3.45-3.612.20.6065730.9640.1750.6321.074100
3.6-3.7912.40.4055830.980.1170.4221.05499.3
3.79-4.0312.40.2695740.9950.0770.2811.08199.7
4.03-4.3412.80.1855940.9970.0530.1931.06199.8
4.34-4.7813.20.1336020.9980.0380.1391.073100
4.78-5.4613.40.1256010.9990.0350.131.048100
5.46-6.87130.1176290.9960.0330.1221.058100
6.87-3010.90.03567010.0110.0371.05997.5

-
Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
AutoSolphasing
RefinementMethod to determine structure: MAD / Resolution: 3.2→29.07 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 0.15 / Phase error: 28.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3257 535 10.01 %
Rwork0.2803 4809 -
obs0.2849 5344 89.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 99.52 Å2 / Biso mean: 26.6217 Å2 / Biso min: 0.95 Å2
Refinement stepCycle: final / Resolution: 3.2→29.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1834 0 10 56 1900
Biso mean--15.75 13.99 -
Num. residues----220
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A489X-RAY DIFFRACTION1.232TORSIONAL
12B489X-RAY DIFFRACTION1.232TORSIONAL
13C489X-RAY DIFFRACTION1.232TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.2-3.520.31681080.3098968107675
3.52-4.030.31541310.26681179131090
4.03-5.070.31961420.25021279142195
5.08-29.070.34591540.30731383153797

+
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