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- PDB-6rvp: SaFtsz-GDP-MetPyr -

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Basic information

Entry
Database: PDB / ID: 6rvp
TitleSaFtsz-GDP-MetPyr
ComponentsCell division protein FtsZ
KeywordsCELL CYCLE / Cell division protein
Function / homology
Function and homology information


FtsZ-dependent cytokinesis / division septum assembly / cell division site / protein polymerization / GTPase activity / GTP binding / cytoplasm
Similarity search - Function
Tubulin-like protein FtsZ/CetZ / 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/FtsZ family, C-terminal domain / Tubulin/FtsZ-like, C-terminal domain / Tubulin/FtsZ, C-terminal ...Tubulin-like protein FtsZ/CetZ / 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/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
GUANOSINE-5'-DIPHOSPHATE / 1-methylpyrrolidin-2-one / Cell division protein FtsZ
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.16 Å
AuthorsFernandez-Tornero, C. / Andreu, J.M.
CitationJournal: Febs J. / Year: 2020
Title: Nucleotide-induced folding of cell division protein FtsZ from Staphylococcus aureus.
Authors: Huecas, S. / Canosa-Valls, A.J. / Araujo-Bazan, L. / Ruiz, F.M. / Laurents, D.V. / Fernandez-Tornero, C. / Andreu, J.M.
History
DepositionMay 31, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 19, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 16, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)32,4074
Polymers31,8251
Non-polymers5823
Water4,179232
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area820 Å2
ΔGint-16 kcal/mol
Surface area13620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.477, 50.079, 88.502
Angle α, β, γ (deg.)90.00, 111.78, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Cell division protein FtsZ /


Mass: 31825.014 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 (E. coli) / References: UniProt: P0A031
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine 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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-MB3 / 1-methylpyrrolidin-2-one / N-Methyl-2-pyrrolidone


Mass: 99.131 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 232 / Source method: isolated from a natural source / Formula: H2O

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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: 2.34 Å3/Da / Density % sol: 47.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 26% PEG 5K MME, 10% EthGly, 0.2 M LI2SO4, 0.1 M Tris pH 8.7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.16→40 Å / Num. obs: 92535 / % possible obs: 91 % / Redundancy: 13.4 % / CC1/2: 0.999 / Net I/σ(I): 13.4
Reflection shellResolution: 1.16→1.22 Å / Num. unique obs: 8143 / CC1/2: 0.635

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6RVN

6rvn


Resolution: 1.16→36.207 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 0.31 / Phase error: 26.28
RfactorNum. reflection% reflection
Rfree0.2083 4732 5.12 %
Rwork0.1907 --
obs0.1916 92479 90.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.16→36.207 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2221 0 36 232 2489
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092275
X-RAY DIFFRACTIONf_angle_d1.1153076
X-RAY DIFFRACTIONf_dihedral_angle_d18.394836
X-RAY DIFFRACTIONf_chiral_restr0.079366
X-RAY DIFFRACTIONf_plane_restr0.006405
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.16-1.17320.4026810.37341439X-RAY DIFFRACTION46
1.1732-1.1870.4071830.37331634X-RAY DIFFRACTION51
1.187-1.20150.3549940.34481834X-RAY DIFFRACTION58
1.2015-1.21670.33781110.32191993X-RAY DIFFRACTION62
1.2167-1.23270.32931110.30722229X-RAY DIFFRACTION69
1.2327-1.24960.31281380.29722524X-RAY DIFFRACTION78
1.2496-1.26740.27111470.28042722X-RAY DIFFRACTION86
1.2674-1.28630.28121690.27033155X-RAY DIFFRACTION98
1.2863-1.30640.28041860.2563162X-RAY DIFFRACTION100
1.3064-1.32790.28621780.25433183X-RAY DIFFRACTION100
1.3279-1.35080.27991570.24673195X-RAY DIFFRACTION99
1.3508-1.37530.25051660.24873251X-RAY DIFFRACTION99
1.3753-1.40180.25211540.2323141X-RAY DIFFRACTION99
1.4018-1.43040.2551740.23953167X-RAY DIFFRACTION97
1.4304-1.46150.25861830.23133163X-RAY DIFFRACTION100
1.4615-1.49550.2241700.22953165X-RAY DIFFRACTION99
1.4955-1.53290.25461820.22613221X-RAY DIFFRACTION99
1.5329-1.57430.23191930.2173206X-RAY DIFFRACTION99
1.5743-1.62070.23841460.21163167X-RAY DIFFRACTION99
1.6207-1.6730.21681680.20443128X-RAY DIFFRACTION97
1.673-1.73280.24641700.20373200X-RAY DIFFRACTION99
1.7328-1.80210.24291790.19853201X-RAY DIFFRACTION100
1.8021-1.88420.2121550.19573218X-RAY DIFFRACTION100
1.8842-1.98350.20391790.19353201X-RAY DIFFRACTION99
1.9835-2.10770.20061570.18243162X-RAY DIFFRACTION97
2.1077-2.27050.19331790.17553191X-RAY DIFFRACTION99
2.2705-2.49890.18521790.17163211X-RAY DIFFRACTION100
2.4989-2.86040.18571900.17933207X-RAY DIFFRACTION99
2.8604-3.60330.20041950.1783183X-RAY DIFFRACTION98
3.6033-36.2250.18241580.16683294X-RAY DIFFRACTION98

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