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- PDB-3vo8: Staphylococcus aureus FtsZ GDP-form -

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Basic information

Entry
Database: PDB / ID: 3vo8
TitleStaphylococcus aureus FtsZ GDP-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, C-terminal domain / Tubulin/FtsZ, GTPase domain / 60s Ribosomal Protein L30; Chain: A; ...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, 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.255 Å
AuthorsMatsui, 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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
B: Cell division protein FtsZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,5156
Polymers82,5482
Non-polymers9674
Water1,802100
1
A: Cell division protein FtsZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7573
Polymers41,2741
Non-polymers4832
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cell division protein FtsZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7573
Polymers41,2741
Non-polymers4832
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.039, 44.079, 85.993
Angle α, β, γ (deg.)96.89, 103.57, 108.00
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Cell division protein FtsZ


Mass: 41274.008 Da / Num. of mol.: 2
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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 1.83 Å3/Da / Density % sol: 32.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2M Lithium sulfate, 0.1M Tris-HCl (pH 8.5), 30% PEG 4000, VAPOR DIFFUSION, SITTING DROP, 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 MX225HE / Detector: CCD / Date: Jun 28, 2010
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.255→50 Å / Num. all: 27584 / Num. obs: 26863 / % possible obs: 97.7 % / Redundancy: 2.9 % / Biso Wilson estimate: 28.67 Å2 / Rmerge(I) obs: 0.083
Reflection shellResolution: 2.25→2.31 Å / Rmerge(I) obs: 0.285 / % possible all: 91.3

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3 Å41.01 Å
Translation3 Å41.01 Å

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Processing

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

2vxy


Resolution: 2.255→40.113 Å / Occupancy max: 1 / Occupancy min: 0.75 / FOM work R set: 0.83 / SU ML: 0.59 / σ(F): 1.97 / Phase error: 24.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.237 1916 7.13 %RANDOM
Rwork0.1877 ---
obs0.1912 26859 97.39 %-
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.079 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 109.57 Å2 / Biso mean: 31.8444 Å2 / Biso min: 12.65 Å2
Baniso -1Baniso -2Baniso -3
1--1.8349 Å20.2541 Å21.2956 Å2
2---0.6009 Å2-0.8738 Å2
3---2.4358 Å2
Refinement stepCycle: LAST / Resolution: 2.255→40.113 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4394 0 58 100 4552
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094499
X-RAY DIFFRACTIONf_angle_d1.1556131
X-RAY DIFFRACTIONf_chiral_restr0.071727
X-RAY DIFFRACTIONf_plane_restr0.004801
X-RAY DIFFRACTIONf_dihedral_angle_d17.3251648
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2547-2.3110.29131300.21841640177089
2.311-2.37350.30941160.2251726184295
2.3735-2.44330.30151510.22421793194496
2.4433-2.52220.30221510.2131721187297
2.5222-2.61230.25571380.20131825196398
2.6123-2.71690.26561370.19281752188998
2.7169-2.84050.27081170.19921825194298
2.8405-2.99020.26521400.21011793193398
2.9902-3.17750.26251550.20591812196799
3.1775-3.42270.27031550.19251805196099
3.4227-3.76690.18911360.16571778191499
3.7669-4.31150.20251290.16841839196899
4.3115-5.42990.18851290.16071830195999
5.4299-40.11980.20151320.18411804193699

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