[English] 日本語
Yorodumi
- PDB-6sat: Cell Division Protein SepF in complex with C-terminal domain of FtsZ -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6sat
TitleCell Division Protein SepF in complex with C-terminal domain of FtsZ
Components
  • Cell division protein FtsZ
  • Cell division protein SepF
KeywordsCELL CYCLE / Cell Division protein
Function / homology
Function and homology information


chloroplast fission / FtsZ-dependent cytokinesis / division septum assembly / cell division site / protein polymerization / GTPase activity / GTP binding / metal ion binding / cytoplasm
Similarity search - Function
Cell division protein SepF / SepF-like protein / Cell division protein SepF/SepF-related / SepF-like superfamily / Cell division protein SepF / Tubulin-like protein FtsZ/CetZ / Cell division protein FtsZ / Cell division protein FtsZ, conserved site / Cell division protein FtsZ, C-terminal / FtsZ family, C-terminal domain ...Cell division protein SepF / SepF-like protein / Cell division protein SepF/SepF-related / SepF-like superfamily / Cell division protein SepF / Tubulin-like protein FtsZ/CetZ / Cell division protein FtsZ / Cell division protein FtsZ, conserved site / Cell division protein FtsZ, C-terminal / FtsZ family, C-terminal domain / FtsZ protein signature 1. / FtsZ protein signature 2. / Translation Initiation Factor IF3 / Tubulin/FtsZ family, C-terminal domain / Tubulin/FtsZ-like, C-terminal domain / Tubulin/FtsZ, C-terminal / Tubulin/FtsZ, 2-layer sandwich domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, GTPase domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Cell division protein FtsZ / Cell division protein SepF
Similarity search - Component
Biological speciesCorynebacterium glutamicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å
AuthorsSogues, A. / Wehenkel, A.M. / Alzari, P.M.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyANR-18-CE11-0017-01 France
CitationJournal: Nat Commun / Year: 2020
Title: Essential dynamic interdependence of FtsZ and SepF for Z-ring and septum formation in Corynebacterium glutamicum.
Authors: Sogues, A. / Martinez, M. / Gaday, Q. / Ben Assaya, M. / Grana, M. / Voegele, A. / VanNieuwenhze, M. / England, P. / Haouz, A. / Chenal, A. / Trepout, S. / Duran, R. / Wehenkel, A.M. / Alzari, P.M.
History
DepositionJul 17, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 11, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 23, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cell division protein SepF
B: Cell division protein SepF
P: Cell division protein FtsZ
Q: Cell division protein FtsZ


Theoretical massNumber of molelcules
Total (without water)22,1934
Polymers22,1934
Non-polymers00
Water2,594144
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3620 Å2
ΔGint-24 kcal/mol
Surface area9200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.670, 46.080, 98.980
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Cell division protein SepF


Mass: 9948.335 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025) (bacteria)
Strain: ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025
Gene: sepF, Cgl2152
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q8NNN6
#2: Protein/peptide Cell division protein FtsZ


Mass: 1148.220 Da / Num. of mol.: 2 / Source method: obtained synthetically
Source: (synth.) Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025) (bacteria)
References: UniProt: P94337
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / 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: 1.83 Å3/Da / Density % sol: 32.88 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: 100 mM sodium acetate, and 30% w/v PEG 4000.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 2, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.6→49.5 Å / Num. obs: 21418 / % possible obs: 96.9 % / Redundancy: 3.6 % / Biso Wilson estimate: 20.42 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 10.3
Reflection shellResolution: 1.6→1.63 Å / Rmerge(I) obs: 0.577 / Num. unique obs: 1075 / % possible all: 98.3

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimlessdata scaling
PHASERphasing
BUSTER2.10.3refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→41.77 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.935 / SU R Cruickshank DPI: 0.11 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.117 / SU Rfree Blow DPI: 0.106 / SU Rfree Cruickshank DPI: 0.102
RfactorNum. reflection% reflectionSelection details
Rfree0.231 1081 5.06 %RANDOM
Rwork0.209 ---
obs0.21 21381 96 %-
Displacement parametersBiso max: 117.72 Å2 / Biso mean: 27.37 Å2 / Biso min: 10.3 Å2
Baniso -1Baniso -2Baniso -3
1-1.3261 Å20 Å20 Å2
2---5.878 Å20 Å2
3---4.5518 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: final / Resolution: 1.6→41.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1441 0 0 144 1585
Biso mean---35.4 -
Num. residues----189
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d502SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes253HARMONIC5
X-RAY DIFFRACTIONt_it1461HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion196SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1786SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1461HARMONIC20.009
X-RAY DIFFRACTIONt_angle_deg1976HARMONIC20.96
X-RAY DIFFRACTIONt_omega_torsion2.88
X-RAY DIFFRACTIONt_other_torsion14.72
LS refinement shellResolution: 1.6→1.61 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.3131 19 4.44 %
Rwork0.3159 409 -
all0.3157 428 -
obs--97.15 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.8759-0.5982-0.00970.6145-0.07761.96070.023-0.11270.19860.01820.007-0.0438-0.1789-0.0582-0.0299-0.13890.00950.0004-0.0724-0.0281-0.119-11.3508-1.04950.3759
23.97774.3087-5.63632.8842-5.22792.4860.0377-0.0368-0.07290.2972-0.1505-0.4924-0.54250.25080.11280.48690.0406-0.06920.1586-0.01630.1787-5.75755.0026-10.7949
30.5207-0.06650.22131.41170.70742.5386-0.00270.00280.0410.12980.0352-0.0568-0.0268-0.1336-0.0325-0.14150.0083-0.0018-0.0628-0.0148-0.1269-5.6819-10.671417.2424
47.1227-0.7419-0.75732.15091.88763.7901-0.1084-0.134-0.24540.05690.06950.09810.0769-0.22860.03890.37710.05690.01710.1520.04160.103-6.2753-20.961925.8805
53.7860.491-0.87791.7808-2.39394.6805-0.0105-0.67610.2353-0.00040.17230.111-0.0026-0.4034-0.1618-0.07690.0227-0.01220.2031-0.0381-0.0336-18.0852-11.81413.4867
62.5553.0671-0.4951.2669-2.03872.76430.0117-0.09070.02940.24690.0308-0.041-0.12830.0692-0.04250.1278-0.08410.0662-0.1956-0.2530.0505-4.95846.30168.8374
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|65 - A|138 }A65 - 138
2X-RAY DIFFRACTION2{ A|139 - A|149 }A139 - 149
3X-RAY DIFFRACTION3{ B|65 - B|138 }B65 - 138
4X-RAY DIFFRACTION4{ B|139 - B|151 }B139 - 151
5X-RAY DIFFRACTION5{ P|434 - P|442 }P434 - 442
6X-RAY DIFFRACTION6{ Q|434 - Q|441 }Q434 - 441

+
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