[English] 日本語
Yorodumi
- PDB-5h5g: Staphylococcus aureus FtsZ-GDP in T and R states -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5h5g
TitleStaphylococcus aureus FtsZ-GDP in T and R states
ComponentsCell division protein FtsZ
KeywordsCELL CYCLE / Tubulin/FtsZ family / GTPase / protofilament
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, C-terminal domain / Tubulin/FtsZ, GTPase domain / 60s Ribosomal Protein L30; Chain: A; ...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, C-terminal domain / Tubulin/FtsZ, GTPase domain / 60s Ribosomal Protein L30; Chain: A; / 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 / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Cell division protein FtsZ
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsFujita, J. / Harada, R. / Maeda, Y. / Saito, Y. / Mizohata, E. / Inoue, T. / Shigeta, Y. / Matsumura, H.
Funding support Japan, 9items
OrganizationGrant numberCountry
The Japan Society for the Promotion of Science15J00589 Japan
The Japan Society for the Promotion of Science26102526 Japan
The Japan Society for the Promotion of Science16H00783 Japan
The Japan Society for the Promotion of Science15J03797 Japan
The Japan Society for the Promotion of Science16H06164 Japan
The Japan Society for the Promotion of Science26107004 Japan
The Japan Society for the Promotion of Science26105012 Japan
The Japan Society for the Promotion of Science24109017 Japan
The Japan Society for the Promotion of Science15H04443 Japan
CitationJournal: J. Struct. Biol. / Year: 2017
Title: Identification of the key interactions in structural transition pathway of FtsZ from Staphylococcus aureus
Authors: Fujita, J. / Harada, R. / Maeda, Y. / Saito, Y. / Mizohata, E. / Inoue, T. / Shigeta, Y. / Matsumura, H.
History
DepositionNov 5, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 24, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cell division protein FtsZ
B: Cell division protein FtsZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,6335
Polymers63,7062
Non-polymers9263
Water3,531196
1
A: Cell division protein FtsZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3363
Polymers31,8531
Non-polymers4832
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area820 Å2
ΔGint-18 kcal/mol
Surface area13310 Å2
MethodPISA
2
B: Cell division protein FtsZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2962
Polymers31,8531
Non-polymers4431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area760 Å2
ΔGint-6 kcal/mol
Surface area13250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.917, 159.023, 44.058
Angle α, β, γ (deg.)90.000, 92.780, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Cell division protein FtsZ


Mass: 31853.025 Da / Num. of mol.: 2 / Fragment: UNP residues 12-316
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (strain MRSA252) (bacteria)
Strain: MRSA252 / Gene: ftsZ, SAR1162 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6GHP9
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 196 / 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: 2.43 Å3/Da / Density % sol: 49.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 100 mM HEPES, 39% w/v PEP629

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: May 17, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 30358 / % possible obs: 100 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.039 / Rrim(I) all: 0.089 / Χ2: 1.043 / Net I/av σ(I): 19.878 / Net I/σ(I): 7.8 / Num. measured all: 156805
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Diffraction-ID% possible all
2.2-2.245.10.51615020.81100
2.24-2.285.10.5110.811100
2.28-2.325.10.4570.831100
2.32-2.375.20.3580.8921100
2.37-2.425.10.3030.9231100
2.42-2.485.20.2660.9441100
2.48-2.545.20.2450.951100
2.54-2.615.20.2250.9641100
2.61-2.695.20.1860.9681100
2.69-2.775.20.160.9821100
2.77-2.875.20.1390.9851100
2.87-2.995.20.1140.9881100
2.99-3.125.20.0910.9921100
3.12-3.295.20.0770.9931100
3.29-3.495.20.0670.9951100
3.49-3.765.20.070.9941100
3.76-4.145.20.0610.9951100
4.14-4.745.20.0450.9971100
4.74-5.975.20.0410.9981100
5.97-5050.0330.999199.4

-
Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VOA

3voa


Resolution: 2.2→44.01 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.927 / SU B: 7.128 / SU ML: 0.176 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.285 / ESU R Free: 0.222
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2447 1479 4.9 %RANDOM
Rwork0.1841 ---
obs0.187 28844 99.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 104.85 Å2 / Biso mean: 42.403 Å2 / Biso min: 20.89 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å2-0.01 Å2
2---0 Å2-0 Å2
3----0.02 Å2
Refinement stepCycle: final / Resolution: 2.2→44.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4420 0 57 196 4673
Biso mean--29.1 42.1 -
Num. residues----612
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0194573
X-RAY DIFFRACTIONr_bond_other_d0.0020.024470
X-RAY DIFFRACTIONr_angle_refined_deg1.3591.9816194
X-RAY DIFFRACTIONr_angle_other_deg0.906310290
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0985622
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.3126.848184
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.61115799
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3031518
X-RAY DIFFRACTIONr_chiral_restr0.0730.2736
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025328
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02920
X-RAY DIFFRACTIONr_mcbond_it2.144.0382473
X-RAY DIFFRACTIONr_mcbond_other2.1394.0362472
X-RAY DIFFRACTIONr_mcangle_it3.4756.0483097
LS refinement shellResolution: 2.201→2.258 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 114 -
Rwork0.243 1933 -
all-2047 -
obs--93.99 %

+
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