[English] 日本語
Yorodumi
- PDB-7on2: SaFtsZ complexed with GDP (soaking in 10 mM CyDTA) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7on2
TitleSaFtsZ complexed with GDP (soaking in 10 mM CyDTA)
ComponentsCell division protein FtsZ
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 / 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 family, C-terminal domain / Tubulin/FtsZ-like, C-terminal domain / Tubulin/FtsZ, C-terminal ...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 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
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: 1.69 Å
AuthorsFernandez-Tornero, C. / Ruiz, F.M. / Andreu, J.M.
CitationJournal: Plos Biol. / Year: 2022
Title: FtsZ filament structures in different nucleotide states reveal the mechanism of assembly dynamics.
Authors: Ruiz, F.M. / Huecas, S. / Santos-Aledo, A. / Prim, E.A. / Andreu, J.M. / Fernandez-Tornero, C.
History
DepositionMay 25, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 20, 2022Group: 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 1.2Jan 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 FtsZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4844
Polymers31,9401
Non-polymers5443
Water2,918162
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1220 Å2
ΔGint-0 kcal/mol
Surface area13540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.402, 50.207, 88.050
Angle α, β, γ (deg.)90.000, 111.418, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

-
Components

#1: Protein Cell division protein FtsZ


Mass: 31940.100 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: ftsZ / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0A031
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 47.05 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
Details: 0.2 M lithium sulphate, 10% (v/v) ethylene glycol, 0.1 M Tris-HCl pH 8.5, and 26% polyethylene glycol 5000 monomethyl ether (+ 10 mM CyDTA for soaking, 23 h)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9787 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 18, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 1.69→40.98 Å / Num. obs: 31990 / % possible obs: 96.53 % / Redundancy: 3.2 % / Biso Wilson estimate: 28.63 Å2 / CC1/2: 0.998 / Net I/σ(I): 13.23
Reflection shellResolution: 1.69→1.75 Å / Mean I/σ(I) obs: 1.97 / Num. unique obs: 2889 / CC1/2: 0.882

-
Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6RVN

6rvn


Resolution: 1.69→40.98 Å / SU ML: 0.2199 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 31.2521
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2471 1550 4.85 %
Rwork0.2039 30425 -
obs0.2061 31975 96.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.75 Å2
Refinement stepCycle: LAST / Resolution: 1.69→40.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2217 0 33 162 2412
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01092277
X-RAY DIFFRACTIONf_angle_d1.21513081
X-RAY DIFFRACTIONf_chiral_restr0.0657368
X-RAY DIFFRACTIONf_plane_restr0.0077406
X-RAY DIFFRACTIONf_dihedral_angle_d20.1344839
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.69-1.740.29371440.26192453X-RAY DIFFRACTION87.41
1.74-1.810.29781380.26322806X-RAY DIFFRACTION98.89
1.81-1.880.33681510.25972785X-RAY DIFFRACTION98.76
1.88-1.960.28381370.25352820X-RAY DIFFRACTION98.04
1.97-2.070.33891300.27532808X-RAY DIFFRACTION97.61
2.07-2.20.36611280.28192801X-RAY DIFFRACTION97.15
2.2-2.370.34381500.2722704X-RAY DIFFRACTION96.03
2.37-2.610.30811260.23962808X-RAY DIFFRACTION96.04
2.61-2.980.2341320.20932745X-RAY DIFFRACTION96.29
2.98-3.760.18671400.17332793X-RAY DIFFRACTION96.89
3.76-40.980.21241740.15312902X-RAY DIFFRACTION98.75
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)
10.1143615953890.055788093244-0.3208606154040.5723218914510.1866426524271.39147082228-0.392623063436-0.1055694725570.7586529008790.20157257680.257948017733-0.1941514491250.088309957515-0.032784629684-0.04082972523750.222945137760.0515116733618-0.1188525899720.241817315155-0.04024239999240.376232302383-1.988934237036.6605506527327.0448756636
20.1424498608460.04037443102850.03181415304410.0598014927716-0.06867506508560.111682588687-0.147703660111-0.1095762691510.600601128053-0.03384785371440.0836614468176-0.217629467576-0.1519395439530.0322408014866-0.0001647190483850.2561132197740.0445255485726-0.1013602015420.264175061723-0.05795706370610.4565648023175.425084840365.1297341955529.7481939123
31.876862064811.3688785345-0.9961523858891.02150146503-0.6238857281911.45356118173-0.363618226639-0.747521957104-0.2726524910470.3203857323890.0109499025038-0.307546078188-0.002888454541280.146268034695-1.081179223520.2915711479170.115277222266-0.1504952293740.373823783573-0.06586233906030.1018433709833.77203273402-7.6505675287738.9910066641
41.13136699270.2554417881970.4998447589660.2470684384720.09496714200480.191343644065-0.245992619142-0.101917781446-0.05369305464950.2453068014130.111027894630.05471340354580.127513820613-0.115413955881-0.002701476870090.2431489343860.0861323055948-0.02424377868950.229654849512-0.02531124582830.153419266384-5.69301049209-4.3194754917828.963498547
50.06835559450570.03572441508920.0431243928130.177283999769-0.05455786421560.203402822615-0.2094255912-0.0683974159274-0.616502316892-0.0111411181287-0.1407818867190.2060281499890.134093724559-0.1256735806090.0003634227547020.2678433435810.03437344658410.02220887481560.260692666874-0.01806337750650.30946442993-5.81527751805-15.274233783725.1338716897
60.349029060779-0.1074197854810.1441206487980.0945048012984-0.1405840127310.175566700145-0.1877164850260.200899907067-0.0888422897898-0.03952716441190.1179056078050.02933010891340.15310759601-0.201607776159-0.002466149628080.2251287621080.0201321074378-0.02162202111620.2820749571-0.02674572508040.210412450525-4.04426174963-5.7420580811412.3541590229
70.259533057288-0.1837305224870.116607185910.1778817289170.1030373196740.3116375910570.08621091301220.1227850710650.00873306844266-0.541996152524-0.04486621949880.110459967691-0.169210861661-0.00451527435133-7.11854283692E-50.2798545225310.0431370586305-0.02871925065810.254964584934-0.0036736200410.277200270141-4.806093926566.1964268932317.2026780108
80.4355174977780.163396986418-0.1664890498470.0814254820191-0.0702498228650.0659818930809-0.0125483960815-0.02232499208780.1910703423620.1675938169150.0168237147490.1067821533110.02203001398010.0386873252704-4.29750266831E-50.2454295971890.0657455865592-0.0171473341750.259083258595-0.01358076651470.298071625559-21.21751257658.6283052441425.7701183551
90.1240458908130.08806166499960.09266626936120.3467170991780.1295354011090.07799437715640.09820197187270.4683202614210.0651047366963-0.215885269558-0.194051633731-0.2891832273460.159424546350.57357485322-0.000944823337020.2608591874730.05517812009530.005590347347260.4430706129380.0263758788220.300740744253-17.13651086889.060648316056.31787122609
100.929085342127-0.8126645719830.08770623223770.7268677096450.1872220348150.7533808070440.02977743502380.230222280875-0.0410946000278-0.05300503284430.009647353252210.0602300583594-0.009156840567930.09073735915435.67923498534E-50.2237718304110.00703869671084-0.03095523226610.289129730845-0.009375552162250.245802413639-22.06320332128.3158899282812.3422633233
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 9 through 32 )9 - 321 - 24
22chain 'A' and (resid 33 through 60 )33 - 6025 - 54
33chain 'A' and (resid 61 through 93 )61 - 9355 - 87
44chain 'A' and (resid 94 through 140 )94 - 14088 - 134
55chain 'A' and (resid 141 through 157 )141 - 157135 - 151
66chain 'A' and (resid 158 through 178 )158 - 178152 - 172
77chain 'A' and (resid 179 through 202 )179 - 202173 - 196
88chain 'A' and (resid 203 through 224 )203 - 224197 - 220
99chain 'A' and (resid 225 through 245 )225 - 245221 - 241
1010chain 'A' and (resid 246 through 315 )246 - 315242 - 311

+
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