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- PDB-3vpa: Staphylococcus aureus FtsZ apo-form -

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Basic information

Entry
Database: PDB / ID: 3vpa
TitleStaphylococcus aureus FtsZ apo-form
ComponentsCell division protein FtsZ
KeywordsCELL CYCLE / FTSZ / GTP-BINDING / TUBULIN HOMOLOG / POLYMERIZATION / GTPASE / CELL DIVISION
Function / homology
Function and homology information


chloroplast fission / 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, GTPase domain / Tubulin/FtsZ family, C-terminal domain / Tubulin/FtsZ-like, C-terminal domain ...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, 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
Cell division protein FtsZ
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.487 Å
AuthorsMatsui, T. / Yamane, J. / Mogi, N. / Yao, M. / Tanaka, I.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Structural reorganization of the bacterial cell-division protein FtsZ from Staphylococcus aureus
Authors: Matsui, T. / Yamane, J. / Mogi, N. / Yamaguchi, H. / Takemoto, H. / Yao, M. / Tanaka, I.
History
DepositionFeb 28, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 29, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2013Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Revision 1.3Nov 8, 2023Group: 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cell division protein FtsZ
B: Cell division protein FtsZ
C: Cell division protein FtsZ
D: Cell division protein FtsZ


Theoretical massNumber of molelcules
Total (without water)127,4124
Polymers127,4124
Non-polymers00
Water2,504139
1
A: Cell division protein FtsZ


Theoretical massNumber of molelcules
Total (without water)31,8531
Polymers31,8531
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cell division protein FtsZ


Theoretical massNumber of molelcules
Total (without water)31,8531
Polymers31,8531
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Cell division protein FtsZ


Theoretical massNumber of molelcules
Total (without water)31,8531
Polymers31,8531
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Cell division protein FtsZ


Theoretical massNumber of molelcules
Total (without water)31,8531
Polymers31,8531
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.485, 81.058, 225.520
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Cell division protein FtsZ /


Mass: 31853.025 Da / Num. of mol.: 4 / Fragment: UNP residues 12-316
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: Mu50 / Gene: ftsZ / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0A029
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 2.64 Å3/Da / Density % sol: 53.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7
Details: 1.0M Lithium chloride, 0.1M Sodium acetate, 30% PEG 6000, 0.34M Sodium Malonate, pH 7.0, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX325HE / Detector: CCD / Date: Nov 17, 2010
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.487→50 Å / Num. all: 48314 / Num. obs: 47665 / % possible obs: 98.7 % / Redundancy: 7.2 % / Biso Wilson estimate: 49.48 Å2 / Rmerge(I) obs: 0.117
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.417 / Mean I/σ(I) obs: 3.2 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOLREPphasing
PHENIX1.7.3_928refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VO9

3vo9


Resolution: 2.487→35.489 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7921 / SU ML: 0.38 / σ(F): 1.36 / Phase error: 27.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2577 2154 4.52 %RANDOM
Rwork0.2097 ---
obs0.2119 47660 98.7 %-
all-48314 --
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.373 Å2 / ksol: 0.326 e/Å3
Displacement parametersBiso max: 118.89 Å2 / Biso mean: 57.391 Å2 / Biso min: 17.96 Å2
Baniso -1Baniso -2Baniso -3
1--1.1006 Å20 Å2-0 Å2
2--1.7574 Å20 Å2
3----0.6568 Å2
Refinement stepCycle: LAST / Resolution: 2.487→35.489 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8353 0 0 139 8492
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0098402
X-RAY DIFFRACTIONf_angle_d1.25611342
X-RAY DIFFRACTIONf_chiral_restr0.0811388
X-RAY DIFFRACTIONf_plane_restr0.0061503
X-RAY DIFFRACTIONf_dihedral_angle_d16.6683063
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4867-2.54450.37411240.30252761288590
2.5445-2.60810.31691320.269530273159100
2.6081-2.67860.34011480.263429923140100
2.6786-2.75740.35691180.266530523170100
2.7574-2.84640.35081760.271130163192100
2.8464-2.9480.361420.268430423184100
2.948-3.0660.34921310.243330553186100
3.066-3.20550.27571490.241830383187100
3.2055-3.37440.26691680.224430383206100
3.3744-3.58560.28921450.209130503195100
3.5856-3.86210.22551470.192231023249100
3.8621-4.25020.23171500.181330543204100
4.2502-4.86390.20381550.15963070322599
4.8639-6.12280.24271400.198931613301100
6.1228-35.49280.19291290.19193048317792

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