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- PDB-7ojc: SaFtsZ(Q48A) complexed with GDP -

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Basic information

Entry
Database: PDB / ID: 7ojc
TitleSaFtsZ(Q48A) complexed with GDP
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, GTPase domain / Tubulin/FtsZ family, C-terminal domain / Tubulin/FtsZ-like, C-terminal domain ...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, 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
GUANOSINE-5'-DIPHOSPHATE / : / Cell division protein FtsZ
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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 14, 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)32,4274
Polymers31,8831
Non-polymers5443
Water3,585199
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1250 Å2
ΔGint-1 kcal/mol
Surface area13680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.804, 50.951, 88.232
Angle α, β, γ (deg.)90.000, 110.991, 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

#1: Protein Cell division protein FtsZ


Mass: 31883.049 Da / Num. of mol.: 1 / Mutation: Q48A
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
#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.: 199 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.35 Å3/Da / Density % sol: 47.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M lithium sulphate, 10% (v/v) ethylene glycol, 0.1 M Tris-HCl pH 8.6, and 26% polyethylene glycol 5000 monomethyl ether

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 26, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.95→40.56 Å / Num. obs: 21687 / % possible obs: 98.55 % / Redundancy: 3.2 % / Biso Wilson estimate: 28.75 Å2 / CC1/2: 0.994 / Net I/σ(I): 9.19
Reflection shellResolution: 1.95→2.02 Å / Mean I/σ(I) obs: 1.78 / Num. unique obs: 2151 / CC1/2: 0.782

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Processing

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

6rvn


Resolution: 1.95→40.56 Å / SU ML: 0.232 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 23.2295
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2212 1112 5.15 %
Rwork0.1736 20494 -
obs0.176 21606 98.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.75 Å2
Refinement stepCycle: LAST / Resolution: 1.95→40.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2217 0 33 199 2449
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00822291
X-RAY DIFFRACTIONf_angle_d0.89543099
X-RAY DIFFRACTIONf_chiral_restr0.0556369
X-RAY DIFFRACTIONf_plane_restr0.0046409
X-RAY DIFFRACTIONf_dihedral_angle_d19.0428844
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.040.34381200.28472484X-RAY DIFFRACTION95.52
2.04-2.140.26251430.21522553X-RAY DIFFRACTION99.3
2.14-2.280.23461540.19452564X-RAY DIFFRACTION99.09
2.28-2.450.24851430.1872573X-RAY DIFFRACTION98.66
2.45-2.70.22921570.17762536X-RAY DIFFRACTION98.93
2.7-3.090.21721370.17212567X-RAY DIFFRACTION98.61
3.09-3.890.19811470.15762574X-RAY DIFFRACTION98.41
3.89-40.560.19641110.15342643X-RAY DIFFRACTION97.45
Refinement TLS params.Method: refined / Origin x: -8.54944762186 Å / Origin y: 0.0494802880554 Å / Origin z: 22.0122934833 Å
111213212223313233
T0.208672889039 Å20.0185487440284 Å20.00958058983092 Å2-0.195365068943 Å2-0.0226463568642 Å2--0.211798476823 Å2
L1.85310639237 °2-0.856367277977 °20.313840386403 °2-0.870071867403 °2-0.161531700929 °2--0.425550299097 °2
S-0.0967779645261 Å °-0.0329053792625 Å °0.121090016183 Å °0.072289179702 Å °0.0457656676452 Å °0.0071616324422 Å °-0.0264303965502 Å °-0.0274836596488 Å °0.057065648723 Å °
Refinement TLS groupSelection details: (chain 'A' and resid 8 through 315)

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