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- PDB-7ohl: SaFtsZ complexed with GDP, BeF3- and Mn2+ -

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Basic information

Entry
Database: PDB / ID: 7ohl
TitleSaFtsZ complexed with GDP, BeF3- and Mn2+
ComponentsCell division protein FtsZ
KeywordsCELL CYCLE / Cell division protein
Function / homology
Function and homology information


division septum assembly / FtsZ-dependent cytokinesis / cell division site / protein polymerization / GTPase activity / GTP binding / cytoplasm
Similarity search - Function
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-like protein FtsZ/CetZ / Tubulin/FtsZ, C-terminal domain / Tubulin/FtsZ, GTPase domain / 60s Ribosomal Protein L30; Chain: A; ...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-like protein FtsZ/CetZ / 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
BERYLLIUM TRIFLUORIDE ION / GUANOSINE-5'-DIPHOSPHATE / : / : / Cell division protein FtsZ
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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 11, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cell division protein FtsZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4325
Polymers33,8291
Non-polymers6034
Water2,108117
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1320 Å2
ΔGint-11 kcal/mol
Surface area13280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.020, 51.490, 88.020
Angle α, β, γ (deg.)90.000, 110.819, 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

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Cell division protein FtsZ / SaFtsZ


Mass: 33829.180 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

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Non-polymers , 5 types, 121 molecules

#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
#3: Chemical ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: BeF3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 45.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Tris-HCl pH 8.8, 25% PEG 5000 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 6, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.75→41.14 Å / Num. obs: 30098 / % possible obs: 98.37 % / Redundancy: 4.7 % / Biso Wilson estimate: 34.19 Å2 / CC1/2: 0.997 / Net I/σ(I): 8.15
Reflection shellResolution: 1.75→1.85 Å / Num. unique obs: 2991 / CC1/2: 0.334

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Processing

Software
NameVersionClassification
XDS1.18.2_3874data reduction
PHENIX1.18.2_3874refinement
MOLREPphasing
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6RVN

6rvn


Resolution: 1.75→41.14 Å / SU ML: 0.2635 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.9715
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2113 1504 5 %
Rwork0.1696 28580 -
obs0.1717 30084 98.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.38 Å2
Refinement stepCycle: LAST / Resolution: 1.75→41.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2201 0 34 117 2352
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.02982256
X-RAY DIFFRACTIONf_angle_d3.23693051
X-RAY DIFFRACTIONf_chiral_restr0.1311365
X-RAY DIFFRACTIONf_plane_restr0.0188401
X-RAY DIFFRACTIONf_dihedral_angle_d14.9684326
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.810.36361360.322586X-RAY DIFFRACTION99.23
1.81-1.870.30031360.30022582X-RAY DIFFRACTION98.41
1.87-1.950.33381360.27732596X-RAY DIFFRACTION98.41
1.95-2.030.25811370.2142603X-RAY DIFFRACTION99.24
2.03-2.140.24341370.19392603X-RAY DIFFRACTION98.88
2.14-2.280.28361360.18552580X-RAY DIFFRACTION98.66
2.28-2.450.21361380.1752608X-RAY DIFFRACTION98.18
2.45-2.70.21331360.17182591X-RAY DIFFRACTION98.7
2.7-3.090.19281350.1742570X-RAY DIFFRACTION97.27
3.09-3.890.1961390.15062640X-RAY DIFFRACTION98.93
3.89-41.140.18031380.14032621X-RAY DIFFRACTION96.27
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)
11.27742260245-0.1631430931150.1772669277240.6217036131940.04194750684040.640683938386-0.111573426433-0.1070795319170.1316578565880.08562418630020.0465070800341-0.0604331888077-0.0239589689989-0.00967799246619-2.78308290209E-50.3072768991820.0442680850555-0.009905425691750.280864567973-0.02752840736550.2970801807790.714362982922-2.4487141053831.1711090193
20.02023909142450.0277773626698-0.009241304323170.03823015522530.01044010500990.02902238534770.111265402536-0.0377972753541-0.339727213426-0.0555737035492-0.221665978505-0.12343557071-0.138714338465-0.0815170724623-1.36269296398E-50.3573055778290.03575113130280.02332236150760.314165371824-0.009408127256150.402334241833-4.94205613026-17.122833153124.963936329
30.172314559509-0.211082607863-0.15302926502-0.1092883273950.01773972982110.01026006926710.002100805752750.08608632191490.065196629052-0.0126743144973-0.001105934345780.038382503576-0.0151887363988-0.03662328335873.73089876377E-50.323134516450.04616510525560.008439059072770.3291439841410.001795212773150.334011989147-9.372494332451.8926415646618.6360690592
40.426608374898-0.508277469220.2284067378830.3321258132880.04623729875130.3567766997150.1014999380340.160756881013-0.0235981240133-0.0577102042743-0.02660821596710.03296924467910.06604489866460.2143559169597.31443266931E-50.3263103490670.03218905500430.001317879666090.40045921357-0.006975209582880.327289091708-20.74055001297.4129913519411.3759289236
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 11 through 140 )11 - 1401 - 132
22chain 'A' and (resid 141 through 155 )141 - 155133 - 147
33chain 'A' and (resid 156 through 223 )156 - 223148 - 215
44chain 'A' and (resid 224 through 315 )224 - 315216 - 307

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