[English] 日本語
Yorodumi
- PDB-7al1: Cell division protein SepF from Methanobrevibacter smithii -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7al1
TitleCell division protein SepF from Methanobrevibacter smithii
ComponentsCell division protein SepF
KeywordsCELL CYCLE / FtsZ-binding protein Membrane-binding protein
Function / homologyCell division protein SepF/SepF-related / SepF-like superfamily / Cell division protein SepF / Cell division protein SepF
Function and homology information
Biological speciesMethanobrevibacter smithii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsSogues, A. / wehenkel, A.M. / Alzari, P.M.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-18-CE11-0017 France
CitationJournal: Nat Commun / Year: 2021
Title: SepF is the FtsZ anchor in archaea, with features of an ancestral cell division system.
Authors: Pende, N. / Sogues, A. / Megrian, D. / Sartori-Rupp, A. / England, P. / Palabikyan, H. / Rittmann, S.K.R. / Grana, M. / Wehenkel, A.M. / Alzari, P.M. / Gribaldo, S.
History
DepositionOct 4, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 31, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 13, 2021Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_database_proc
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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cell division protein SepF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,9742
Polymers10,8511
Non-polymers1221
Water1,02757
1
A: Cell division protein SepF
hetero molecules

A: Cell division protein SepF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9474
Polymers21,7032
Non-polymers2442
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area2300 Å2
ΔGint-14 kcal/mol
Surface area9310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.053, 53.053, 53.912
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-305-

HOH

21A-348-

HOH

-
Components

#1: Protein Cell division protein SepF


Mass: 10851.482 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanobrevibacter smithii (strain ATCC 35061 / DSM 861 / OCM 144 / PS) (archaea)
Strain: ATCC 35061 / DSM 861 / OCM 144 / PS / Gene: Msm_0406 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A5UK83
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 2.02 Å3/Da / Density % sol: 39.06 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1 M TRIS, pH 8.5, 30% PEG 10K

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9875 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9875 Å / Relative weight: 1
ReflectionResolution: 1.4→45.95 Å / Num. obs: 17704 / % possible obs: 99.9 % / Redundancy: 19.6 % / Biso Wilson estimate: 20.19 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 27.1
Reflection shellResolution: 1.4→1.42 Å / Rmerge(I) obs: 1.029 / Mean I/σ(I) obs: 3.4 / Num. unique obs: 846

-
Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimless0.7.4data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb code 3ZIE

3zie


Resolution: 1.4→34.97 Å / SU ML: 0.1155 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.0207
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2163 884 5 %
Rwork0.1825 16789 -
obs0.1842 17673 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.38 Å2
Refinement stepCycle: LAST / Resolution: 1.4→34.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms662 0 8 57 727
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092702
X-RAY DIFFRACTIONf_angle_d1.0567952
X-RAY DIFFRACTIONf_chiral_restr0.0839115
X-RAY DIFFRACTIONf_plane_restr0.0065120
X-RAY DIFFRACTIONf_dihedral_angle_d18.9164103
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.490.25491440.22082746X-RAY DIFFRACTION99.9
1.49-1.60.2371450.2082759X-RAY DIFFRACTION100
1.6-1.760.26641460.19672773X-RAY DIFFRACTION100
1.76-2.020.23851460.17682774X-RAY DIFFRACTION99.97
2.02-2.540.16631490.17862830X-RAY DIFFRACTION99.97
2.54-34.970.22331540.1792907X-RAY DIFFRACTION99.54
Refinement TLS params.Method: refined / Origin x: -4.29269921737 Å / Origin y: -22.3702062537 Å / Origin z: 8.34574490984 Å
111213212223313233
T0.161744024712 Å2-0.018976800801 Å20.0115410230988 Å2-0.182588589369 Å20.00890331244746 Å2--0.192529524707 Å2
L0.482168890831 °2-0.0892177469441 °20.46508982797 °2-1.3292086124 °2-0.381700313415 °2--1.1293976508 °2
S0.0465287058532 Å °-0.0931985426233 Å °0.00297075997274 Å °0.0160879674488 Å °-0.0580051748327 Å °-0.258204156421 Å °0.0312984829032 Å °-0.0266242905909 Å °-0.00119555859279 Å °

+
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