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- PDB-7oi2: SaFtsz complexed with GDP (NaCl purification) -

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Basic information

Entry
Database: PDB / ID: 7oi2
TitleSaFtsz complexed with GDP (NaCl purification)
ComponentsCell division protein FtsZ
KeywordsCELL CYCLE / Cell division
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
GUANOSINE-5'-DIPHOSPHATE / Cell division protein FtsZ
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsFernandez-Tornero, C. / Ruiz, F.M. / Andreu Morales, 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

Downloads & links

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Assembly

Deposited unit
A: Cell division protein FtsZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3574
Polymers33,8291
Non-polymers5283
Water3,729207
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1120 Å2
ΔGint-11 kcal/mol
Surface area13550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.187, 53.754, 85.349
Angle α, β, γ (deg.)90.000, 108.212, 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 / 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
#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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na / 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 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 207 / Source method: isolated from a natural source / Formula: H2O
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: 2.22 Å3/Da / Density % sol: 44.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Tris-HCl pH 8, 25% PEG5000 MME

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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: Dec 4, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.9→41.61 Å / Num. obs: 23465 / % possible obs: 99.32 % / Redundancy: 3.4 % / Biso Wilson estimate: 30.07 Å2 / CC1/2: 0.999 / Net I/σ(I): 14.4
Reflection shellResolution: 1.9→1.96 Å / Mean I/σ(I) obs: 1.72 / Num. unique obs: 2315 / CC1/2: 0.759

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Processing

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

6rvn


Resolution: 1.9→41.61 Å / SU ML: 0.2629 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.4499
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2337 1203 5.13 %
Rwork0.1721 22253 -
obs0.1751 23456 99.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.76 Å2
Refinement stepCycle: LAST / Resolution: 1.9→41.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2217 0 33 207 2457
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00672305
X-RAY DIFFRACTIONf_angle_d0.943123
X-RAY DIFFRACTIONf_chiral_restr0.0583373
X-RAY DIFFRACTIONf_plane_restr0.0042412
X-RAY DIFFRACTIONf_dihedral_angle_d20.5306858
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.980.37521410.28932448X-RAY DIFFRACTION99.92
1.98-2.070.31331290.22562457X-RAY DIFFRACTION99.65
2.07-2.170.25621310.20872463X-RAY DIFFRACTION99.5
2.17-2.310.25651390.19682482X-RAY DIFFRACTION99.66
2.31-2.490.2631410.17862438X-RAY DIFFRACTION99.58
2.49-2.740.25261450.17962482X-RAY DIFFRACTION99.55
2.74-3.140.23671370.17382487X-RAY DIFFRACTION99.58
3.14-3.950.18811330.15682464X-RAY DIFFRACTION98.78
3.95-41.610.2031070.14482532X-RAY DIFFRACTION97.78
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)
13.45010486714-0.400634163801-0.2837698435011.852994851770.7645187563981.853942937-0.17643914308-0.3863235354360.2850602219780.229978333970.174484784505-0.263181349891-0.05648595255920.0233384983244-0.02252165519340.2615508610870.0585393681066-0.04153414077250.235500065645-0.04538633677840.2110421083912.2558360544-0.03198127316832.2319555062
22.14123385707-1.04472724998-0.3019769609231.559551810140.4329050632250.992559661457-0.031803601544-0.01379906383290.0454349406806-0.002051320676230.0122332965710.0141627753086-0.108665722422-0.08592603641450.01646637513870.1884469547350.00836394839967-0.008917820758560.183853057784-0.0133690616940.182899542786-7.18418493951-1.5644481081319.9659943439
32.62055713017-2.314320988080.4452263144553.25536143178-0.07192686685993.02908131860.1250135473410.3312110627520.0282657355006-0.197054464526-0.220335141053-0.09761990593310.03441472350740.225875524350.06720223176040.1861884715050.02504545396750.007129484753160.286411393007-0.01149822719870.211380404054-19.67283806958.4032002795610.8046201816
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 124 )9 - 1241 - 118
22chain 'A' and (resid 125 through 224 )125 - 224119 - 222
33chain 'A' and (resid 225 through 315 )225 - 315223 - 319

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