[English] 日本語
Yorodumi
- PDB-3vo9: Staphylococcus aureus FtsZ apo-form (SeMet) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3vo9
TitleStaphylococcus aureus FtsZ apo-form (SeMet)
ComponentsCell division protein FtsZ
KeywordsCELL CYCLE / FTSZ / GTP-BINDING / TUBULIN HOMOLOG / POLYMERIZATION / GTPASE / CELL DIVISION
Function / homology
Function and homology information


chloroplast fission / FtsZ-dependent cytokinesis / division septum assembly / cell division site / protein polymerization / GTPase activity / GTP binding / cytoplasm
Similarity search - Function
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. / Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ family, C-terminal domain / Tubulin/FtsZ-like, C-terminal domain ...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. / Tubulin/FtsZ, GTPase domain / 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 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Cell division protein FtsZ
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.706 Å
AuthorsMatsui, T. / Yamane, J. / Mogi, N. / Yao, M. / Tanaka, I.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Structural reorganization of the bacterial cell-division protein FtsZ from Staphylococcus aureus
Authors: Matsui, T. / Yamane, J. / Mogi, N. / Yamaguchi, H. / Takemoto, H. / Yao, M. / Tanaka, I.
History
DepositionJan 20, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 29, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2013Group: Database references

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cell division protein FtsZ
B: Cell division protein FtsZ
C: Cell division protein FtsZ
D: Cell division protein FtsZ


Theoretical massNumber of molelcules
Total (without water)129,8514
Polymers129,8514
Non-polymers00
Water1,38777
1
A: Cell division protein FtsZ


Theoretical massNumber of molelcules
Total (without water)32,4631
Polymers32,4631
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cell division protein FtsZ


Theoretical massNumber of molelcules
Total (without water)32,4631
Polymers32,4631
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Cell division protein FtsZ


Theoretical massNumber of molelcules
Total (without water)32,4631
Polymers32,4631
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Cell division protein FtsZ


Theoretical massNumber of molelcules
Total (without water)32,4631
Polymers32,4631
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.692, 79.987, 225.718
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
Cell division protein FtsZ /


Mass: 32462.658 Da / Num. of mol.: 4 / Fragment: UNP residues 12-316
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: Mu50 / Gene: ftsZ / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0A029
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 77 / 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: 2.57 Å3/Da / Density % sol: 52.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.0M Lithium chloride, 0.1M Sodium acetate, 30% PEG 6000, 0.34M Sodium Malonate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 15, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.706→50 Å / Num. all: 36669 / Num. obs: 36669 / % possible obs: 99.6 % / Redundancy: 14.3 % / Biso Wilson estimate: 47.33 Å2 / Rmerge(I) obs: 0.123
Reflection shellResolution: 2.7→2.8 Å / Rmerge(I) obs: 0.485 / Mean I/σ(I) obs: 5.2 / % possible all: 100

-
Phasing

PhasingMethod: SAD
Phasing dmFOM : 0.7 / FOM acentric: 0.71 / FOM centric: 0.62 / Reflection: 43169 / Reflection acentric: 38513 / Reflection centric: 4656
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
2.6-2.70.380.390.379627349613
2.7-3.20.610.620.4812888117801108
3.2-3.70.840.850.7272736558715
3.7-4.60.880.90.7472686432836
4.6-7.30.880.910.7558994994905

-
Processing

Software
NameVersionClassificationNB
SHELXphasing
RESOLVE2.15phasing
PHENIX1.7.2_869refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.7.2_869phasing
RefinementMethod to determine structure: SAD / Resolution: 2.706→31.764 Å / Occupancy max: 1 / Occupancy min: 0.6 / FOM work R set: 0.791 / SU ML: 0.87 / σ(F): 0 / Phase error: 27.15 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2717 1621 4.56 %RANDOM
Rwork0.2272 33961 --
obs0.2292 35582 96.76 %-
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 21.143 Å2 / ksol: 0.323 e/Å3
Displacement parametersBiso max: 138.9 Å2 / Biso mean: 47.9701 Å2 / Biso min: 17.72 Å2
Baniso -1Baniso -2Baniso -3
1--0.3893 Å20 Å2-0 Å2
2--9.4903 Å20 Å2
3----9.101 Å2
Refinement stepCycle: LAST / Resolution: 2.706→31.764 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8452 0 0 77 8529
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0128503
X-RAY DIFFRACTIONf_angle_d1.24611480
X-RAY DIFFRACTIONf_chiral_restr0.0751403
X-RAY DIFFRACTIONf_plane_restr0.0051523
X-RAY DIFFRACTIONf_dihedral_angle_d17.8813104
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7058-2.78540.37391080.36082449255785
2.7854-2.87520.39161160.33892519263588
2.8752-2.97790.33581290.3262691282093
2.9779-3.09710.33631370.27052847298499
3.0971-3.23790.31181400.258528853025100
3.2379-3.40840.28841390.246128923031100
3.4084-3.62170.26141410.219929213062100
3.6217-3.90080.26881410.208529033044100
3.9008-4.29250.25081370.201129173054100
4.2925-4.91170.20091440.176229593103100
4.9117-6.18080.29971430.224329663109100
6.1808-31.76670.22981460.19523012315896

+
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