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- PDB-7omq: SaFtsZ complexed with GDPPCP and Mn2+ -

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Basic information

Entry
Database: PDB / ID: 7omq
TitleSaFtsZ complexed with GDPPCP 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 family, C-terminal domain / Tubulin/FtsZ-like, C-terminal domain / Tubulin/FtsZ, C-terminal ...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 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
PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / : / 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 24, 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)32,7026
Polymers31,9401
Non-polymers7625
Water3,675204
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1530 Å2
ΔGint5 kcal/mol
Surface area13930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.890, 52.055, 87.937
Angle α, β, γ (deg.)90.000, 110.336, 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: 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-GCP / PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER


Mass: 521.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: GMP-PCP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 204 / 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: 2.37 Å3/Da / Density % sol: 48.15 %
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 22% polyethylene glycol 5000 monomethyl ether (+ 20 mM MnCl2 for soaking, 23h)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.45→40.98 Å / Num. obs: 52628 / % possible obs: 98.68 % / Redundancy: 4.4 % / Biso Wilson estimate: 20.77 Å2 / CC1/2: 0.998 / Net I/σ(I): 9.88
Reflection shellResolution: 1.45→1.5 Å / Mean I/σ(I) obs: 1.11 / Num. unique obs: 5227 / CC1/2: 0.62

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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: 1.45→40.98 Å / SU ML: 0.1857 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.5089
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1868 2571 4.89 %
Rwork0.1611 49994 -
obs0.1624 52565 98.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.63 Å2
Refinement stepCycle: LAST / Resolution: 1.45→40.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2217 0 45 204 2466
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082334
X-RAY DIFFRACTIONf_angle_d1.14683159
X-RAY DIFFRACTIONf_chiral_restr0.079373
X-RAY DIFFRACTIONf_plane_restr0.0063417
X-RAY DIFFRACTIONf_dihedral_angle_d15.3047860
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.480.36191510.31342756X-RAY DIFFRACTION98.61
1.48-1.510.27541560.28322740X-RAY DIFFRACTION98.77
1.51-1.540.311150.27392777X-RAY DIFFRACTION98.47
1.54-1.580.28851420.25362786X-RAY DIFFRACTION98.45
1.58-1.620.25961310.24562728X-RAY DIFFRACTION98.05
1.62-1.660.23411380.21032767X-RAY DIFFRACTION99.35
1.66-1.710.23661450.20372782X-RAY DIFFRACTION99.66
1.71-1.760.22521230.19632833X-RAY DIFFRACTION99.13
1.76-1.830.24251310.18582779X-RAY DIFFRACTION98.85
1.83-1.90.19461290.18432783X-RAY DIFFRACTION98.68
1.9-1.990.19561340.17332726X-RAY DIFFRACTION96.79
1.99-2.090.20291490.15612776X-RAY DIFFRACTION98.58
2.09-2.220.17251350.15412793X-RAY DIFFRACTION99.69
2.22-2.40.19051550.14982780X-RAY DIFFRACTION99.12
2.4-2.640.17551600.14932774X-RAY DIFFRACTION99.22
2.64-3.020.18881520.15022753X-RAY DIFFRACTION97.48
3.02-3.80.15781560.14132818X-RAY DIFFRACTION99.4
3.8-40.980.1631690.13822843X-RAY DIFFRACTION98.14
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)
12.06948145257-0.7000963004010.1757972247041.413444364860.4012080974661.58957934473-0.0605361054981-0.01922178638480.1617612299120.0534318398662-0.0114472730124-0.0513206020813-0.1558940094920.03637828812160.0497838495270.160317935990.0124211101899-0.01431788439430.1350385462890.003344627451530.1487181458690.704356363841-1.9061953787831.2606120393
24.07796197151-1.70135844688-1.829230887114.954317144411.91537081954.78272459991-0.06013614447880.0165917541262-0.5318006745760.0375004359424-0.2554875952370.3909932296080.208125186603-0.1046343866320.3019557128440.1660581020420.0153623873232-0.007895698390040.141590426753-0.007696181822230.225419294649-5.78127365667-15.972800101425.8664788671
31.111831403-0.642820153831-0.5982794396680.694953882590.578786339670.6138377569160.0221366227980.1049225867390.0874065467458-0.0586314037392-0.03647005038830.0319894966262-0.0692039173472-0.0409314433648-0.001410353470940.2304226163420.0535935934585-0.02827842813310.2374040735390.001792844457520.193713491303-9.115889592961.9223521844618.0501430846
41.753579332-1.868453485920.8814640746242.75872413285-0.5954320810031.809617551940.2321922793890.306366422121-0.116864716349-0.275747013093-0.2143191428630.109461136080.08972141771080.244234272007-0.01746041174930.2037700355730.0553634513862-0.0002153824138510.324040960698-0.01148365978810.202516890945-20.20804297177.1269559284410.8959769011
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 - 133
22chain 'A' and (resid 141 through 157 )141 - 157134 - 151
33chain 'A' and (resid 158 through 223 )158 - 223152 - 222
44chain 'A' and (resid 224 through 315 )224 - 315223 - 317

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