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- PDB-3voa: Staphylococcus aureus FtsZ 12-316 GDP-form -

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Basic information

Entry
Database: PDB / ID: 3voa
TitleStaphylococcus aureus FtsZ 12-316 GDP-form
ComponentsCell division protein FtsZ
KeywordsCELL CYCLE / FTSZ / GTP-BINDING / TUBULIN HOMOLOG / POLYMERIZATION / GTPASE / 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 / MOLECULAR REPLACEMENT / Resolution: 1.73 Å
AuthorsYamane, J. / Matsui, T. / 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
DepositionJan 20, 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 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)32,3363
Polymers31,8531
Non-polymers4832
Water4,774265
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.828, 49.551, 88.413
Angle α, β, γ (deg.)90.000, 111.570, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Cell division protein FtsZ


Mass: 31853.025 Da / Num. of mol.: 1 / 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: Chemical ChemComp-GDP / GUANOSINE-5'-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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 265 / 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: 47.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2M Lithium sulfate, 0.1M Tris-HCl, 25% PEG 5000MME, 10% ethylene glycol, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: May 17, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.73→50 Å / Num. all: 30763 / Num. obs: 29340 / % possible obs: 95.4 % / Redundancy: 2.7 % / Biso Wilson estimate: 20.02 Å2 / Rmerge(I) obs: 0.05
Reflection shellResolution: 1.73→1.78 Å / Rmerge(I) obs: 0.149 / Mean I/σ(I) obs: 4.5 / % possible all: 90.3

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Processing

Software
NameVersionClassificationNB
PHENIX1.7.2_869refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2VXY

2vxy


Resolution: 1.73→19.995 Å / Occupancy max: 1 / Occupancy min: 0.66 / FOM work R set: 0.8654 / SU ML: 0.35 / σ(F): 0 / Phase error: 20.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2299 1485 5.1 %RANDOM
Rwork0.1878 ---
obs0.1899 29132 94.7 %-
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.479 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 58.68 Å2 / Biso mean: 23.4949 Å2 / Biso min: 10.73 Å2
Baniso -1Baniso -2Baniso -3
1--1.8465 Å2-0 Å2-4.1198 Å2
2--3.224 Å20 Å2
3----1.3775 Å2
Refinement stepCycle: LAST / Resolution: 1.73→19.995 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2215 0 29 265 2509
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072268
X-RAY DIFFRACTIONf_angle_d1.1473074
X-RAY DIFFRACTIONf_chiral_restr0.072365
X-RAY DIFFRACTIONf_plane_restr0.004403
X-RAY DIFFRACTIONf_dihedral_angle_d14.895830
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7304-1.78630.27631320.22532276240887
1.7863-1.85010.25221450.19882473261894
1.8501-1.92410.22391310.18722535266695
1.9241-2.01160.25891500.18712522267297
2.0116-2.11750.22761360.18412557269398
2.1175-2.250.22971330.18352603273698
2.25-2.42350.22421530.18562602275599
2.4235-2.66680.24661460.18482601274798
2.6668-3.05160.22031210.19852613273497
3.0516-3.84020.24531040.18762361246587
3.8402-19.99650.20441340.18092504263892

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