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- PDB-3wgn: STAPHYLOCOCCUS AUREUS FTSZ bound with GTP-gamma-S -

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Basic information

Entry
Database: PDB / ID: 3wgn
TitleSTAPHYLOCOCCUS AUREUS FTSZ bound with GTP-gamma-S
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
5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE / Cell division protein FtsZ
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.606 Å
AuthorsMatsui, T. / Mogi, N. / Tanaka, I. / Yao, M.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Structural change in FtsZ Induced by intermolecular interactions between bound GTP and the T7 loop
Authors: Matsui, T. / Han, X. / Yu, J. / Yao, M. / Tanaka, I.
History
DepositionAug 6, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 25, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2014Group: 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
B: Cell division protein FtsZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,6274
Polymers82,5482
Non-polymers1,0782
Water00
1
A: Cell division protein FtsZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8132
Polymers41,2741
Non-polymers5391
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cell division protein FtsZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8132
Polymers41,2741
Non-polymers5391
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.270, 44.170, 73.280
Angle α, β, γ (deg.)82.840, 82.810, 82.340
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-GSP / 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE


Mass: 539.246 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3S

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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: 1.696 Å3/Da / Density % sol: 27.498 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 1.0M Lithium chloride, 0.1M Sodium acetate, 30%(w/v) PEG6000, 10%(v/v) glycerol, 5mM GTPgammaS, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 4, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.606→50 Å / Num. obs: 16267 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 53.716 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 11.79
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.61-2.760.8170.612.439840266525770.7196.7
2.76-2.950.9030.4193.589554248024380.48598.3
2.95-3.190.9660.2465.929022234023060.28598.5
3.19-3.490.9890.149.328268214921240.16398.8
3.49-3.90.9930.08614.857381194219250.199.1
3.9-4.50.9950.05820.516431174617160.06898.3
4.5-5.490.9960.05222.485298144114310.06199.3
5.49-7.710.9970.04524.214150112111090.05398.9
7.710.9980.03332.1124126456410.03899.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
MOLREPphasing
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
XDSdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3voa

3voa


Resolution: 2.606→43.511 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7034 / SU ML: 0.52 / σ(F): 2 / Phase error: 35.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2799 814 5.01 %RANDOM
Rwork0.228 ---
obs0.2306 16263 98.41 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 89.35 Å2 / Biso mean: 38.0887 Å2 / Biso min: 16.81 Å2
Refinement stepCycle: LAST / Resolution: 2.606→43.511 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4386 0 64 0 4450
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0124486
X-RAY DIFFRACTIONf_angle_d1.5916072
X-RAY DIFFRACTIONf_chiral_restr0.089726
X-RAY DIFFRACTIONf_plane_restr0.007798
X-RAY DIFFRACTIONf_dihedral_angle_d16.4671650
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6064-2.76960.38621330.36222529266297
2.7696-2.98340.42631340.33982546268098
2.9834-3.28360.34161350.30482553268899
3.2836-3.75850.33991380.24842618275699
3.7585-4.73440.26151360.18892600273699
4.7344-43.51720.17741380.16062603274199

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