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- PDB-3vob: Staphylococcus aureus FtsZ with PC190723 -

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Basic information

Entry
Database: PDB / ID: 3vob
TitleStaphylococcus aureus FtsZ with PC190723
ComponentsCell division protein FtsZ
KeywordsCELL CYCLE/INHIBITOR / FTSZ / GTP-BINDING / TUBULIN HOMOLOG / POLYMERIZATION / GTPASE / CELL DIVISION / CELL CYCLE-INHIBITOR complex
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
Chem-9PC / GUANOSINE-5'-DIPHOSPHATE / Cell division protein FtsZ
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.703 Å
AuthorsYamane, J. / Matsui, T. / Mogi, N. / Yamaguchi, H. / Takemoto, H. / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_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_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6924
Polymers31,8531
Non-polymers8393
Water79344
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.095, 50.507, 88.288
Angle α, β, γ (deg.)90.00, 110.95, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-512-

HOH

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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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: 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
#4: Chemical ChemComp-9PC / 3-[(6-chloro[1,3]thiazolo[5,4-b]pyridin-2-yl)methoxy]-2,6-difluorobenzamide / PC190723


Mass: 355.747 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H8ClF2N3O2S
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 2.39 Å3/Da / Density % sol: 48.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2M Lithium sulfate, 0.1M Tris-HCl, 25% PEG5000MME, 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: Jul 1, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.703→50 Å / Num. all: 8292 / Num. obs: 8237 / % possible obs: 99.8 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.115
Reflection shellResolution: 2.7→2.8 Å / Rmerge(I) obs: 0.352 / Mean I/σ(I) obs: 3.9 / % possible all: 99.8

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Phasing

PhasingMethod: molecular replacement

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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: 3VO8

3vo8


Resolution: 2.703→32.351 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8284 / SU ML: 0.85 / σ(F): 1.35 / Phase error: 24.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2467 571 6.93 %RANDOM
Rwork0.1948 ---
obs0.1985 8236 99.42 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 3.414 Å2 / ksol: 0.302 e/Å3
Displacement parametersBiso max: 60.85 Å2 / Biso mean: 25.6982 Å2 / Biso min: 11.92 Å2
Baniso -1Baniso -2Baniso -3
1-1.3418 Å20 Å20.1608 Å2
2---0.3615 Å2-0 Å2
3----0.9803 Å2
Refinement stepCycle: LAST / Resolution: 2.703→32.351 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2193 0 52 44 2289
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0152268
X-RAY DIFFRACTIONf_angle_d1.3883071
X-RAY DIFFRACTIONf_chiral_restr0.079363
X-RAY DIFFRACTIONf_plane_restr0.004402
X-RAY DIFFRACTIONf_dihedral_angle_d19.401826
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7032-2.97510.32881440.25971879202398
2.9751-3.40520.24261290.216919172046100
3.4052-4.28860.23171450.169719092054100
4.2886-32.35360.22321530.173519602113100

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