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- PDB-7ohh: SaFtsZ complexed with GDP and BeF3- -

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Basic information

Entry
Database: PDB / ID: 7ohh
TitleSaFtsZ complexed with GDP and BeF3-
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: 1.45 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

Downloads & links

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Assembly

Deposited unit
A: Cell division protein FtsZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3774
Polymers33,8291
Non-polymers5483
Water3,999222
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1180 Å2
ΔGint-5 kcal/mol
Surface area13420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.750, 51.060, 87.840
Angle α, β, γ (deg.)90.000, 111.032, 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: 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 (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-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-K / POTASSIUM ION


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


Mass: 18.015 Da / Num. of mol.: 222 / 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: 2.21 Å3/Da / Density % sol: 44.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Tris-HCl pH 8.8, 28% PEG 5000 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: Jun 27, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.45→40.99 Å / Num. obs: 51784 / % possible obs: 98.13 % / Redundancy: 3.9 % / Biso Wilson estimate: 25.89 Å2 / CC1/2: 0.998 / Net I/σ(I): 12.83
Reflection shellResolution: 1.45→1.502 Å / Num. unique obs: 5181 / CC1/2: 0.306

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Processing

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

6rvn


Resolution: 1.45→40.99 Å / SU ML: 0.3011 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.0484
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2073 2585 5 %
Rwork0.1774 49134 -
obs0.1789 51719 98.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.73 Å2
Refinement stepCycle: LAST / Resolution: 1.45→40.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2217 0 33 222 2472
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00932288
X-RAY DIFFRACTIONf_angle_d1.18193097
X-RAY DIFFRACTIONf_chiral_restr0.0795369
X-RAY DIFFRACTIONf_plane_restr0.0066408
X-RAY DIFFRACTIONf_dihedral_angle_d18.4677847
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.480.74141430.75442722X-RAY DIFFRACTION98.39
1.48-1.510.5221440.5842745X-RAY DIFFRACTION98.94
1.51-1.540.46141430.43432715X-RAY DIFFRACTION98.48
1.54-1.580.33951450.36042746X-RAY DIFFRACTION98.53
1.58-1.620.33081410.30112683X-RAY DIFFRACTION98.47
1.62-1.660.30641440.25922729X-RAY DIFFRACTION98.12
1.66-1.710.28311430.24582728X-RAY DIFFRACTION98.02
1.71-1.760.26741430.23442734X-RAY DIFFRACTION98.36
1.76-1.830.24921430.20952718X-RAY DIFFRACTION98.32
1.83-1.90.23031440.17762740X-RAY DIFFRACTION98.83
1.9-1.990.21951440.172728X-RAY DIFFRACTION98.66
1.99-2.090.20961410.16122693X-RAY DIFFRACTION97.29
2.09-2.220.20781450.16092740X-RAY DIFFRACTION98.03
2.22-2.390.18431440.15972734X-RAY DIFFRACTION98.8
2.39-2.630.17991430.15252725X-RAY DIFFRACTION98.02
2.63-3.020.17961430.16192710X-RAY DIFFRACTION96.22
3.02-3.80.17381450.15612762X-RAY DIFFRACTION98.34
3.8-40.990.18541470.1512782X-RAY DIFFRACTION96.6
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)
12.81044648254-0.7912049828560.2156510961241.288447480730.3441740494550.893782028158-0.241966490701-0.386005641790.3895416003940.1976068613420.177583065492-0.200887993384-0.116744035837-0.02441324946240.01647082882010.2206731862470.0808261494558-0.03363965439040.205010133003-0.06347958246570.201114758750.145683080967-2.4431234951131.4253982559
24.54996459172-6.05302788282-4.354778037458.359627273255.69449048714.18983582942-0.295599974123-0.138296138325-0.5600667797240.14633363729-0.01956595640290.2946092877120.143349816247-0.03473970554130.431350176340.2812806795090.03009991545240.02720121924560.2452075504730.01739445581520.28719090889-5.69736540107-16.567824160525.244094439
31.93011054666-1.02881117561-0.7877953880550.6818184363450.6599444910560.44533975504-0.02485297352660.02979133781480.203263647883-0.04906172266060.0259656487922-0.0273536068043-0.106142421215-0.04235404086180.002744589640130.2215817994480.0370525130935-0.009433282489420.220266036133-0.006346779466250.212111651529-9.544736978642.1526060011318.4682747291
42.24133059808-2.305095437711.034946982333.4983793919-0.5001958311782.6968920840.1735921544690.205449839351-0.0700075319214-0.152452193349-0.0929018839524-0.00553797908950.1577589582250.236948867096-0.08413353982280.1499426559720.01245151360540.00600500351450.235144551634-0.0157168217590.192420151872-20.75354481537.4826912051811.3038921057
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 140 )9 - 1401 - 136
22chain 'A' and (resid 141 through 157 )141 - 157137 - 153
33chain 'A' and (resid 158 through 223 )158 - 223154 - 221
44chain 'A' and (resid 224 through 315 )224 - 315222 - 313

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