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- PDB-3wgk: STAPHYLOCOCCUS AUREUS FTSZ T7 mutant substituted for GAG, DeltaT7... -

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Basic information

Entry
Database: PDB / ID: 3wgk
TitleSTAPHYLOCOCCUS AUREUS FTSZ T7 mutant substituted for GAG, DeltaT7GAG-GDP
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.799 Å
AuthorsHan, X. / Matsui, T. / Yu, J. / 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 22, 2017Group: Refinement description / Category: software
Revision 1.3Nov 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

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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)82,8324
Polymers81,9452
Non-polymers8862
Water00
1
A: Cell division protein FtsZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4162
Polymers40,9731
Non-polymers4431
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cell division protein FtsZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4162
Polymers40,9731
Non-polymers4431
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.335, 95.927, 72.136
Angle α, β, γ (deg.)90.000, 100.870, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Cell division protein FtsZ


Mass: 40972.711 Da / Num. of mol.: 2 / Mutation: 204SGEVN208 to GAG
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.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
Sequence detailsUNP RESIDUES 204-208 (SGEVN) WERE REPLACED WITH GAG.

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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: 1.84 Å3/Da / Density % sol: 33.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2M Sodium Acetate, 0.1M Tris-HCl, 30%(w/v) PEG4000, 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: Jul 4, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.799→50 Å / Num. obs: 14645 / % possible obs: 99.7 % / Redundancy: 3.8 % / Biso Wilson estimate: 83.82 Å2 / Rmerge(I) obs: 0.093 / Χ2: 4.859
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.8-2.93.70.4314411.421199.7
2.9-3.023.80.31214701.5951100
3.02-3.153.80.22914681.8681100
3.15-3.323.80.15614542.1561100
3.32-3.533.80.11414693.0141100
3.53-3.83.80.09414504.021100
3.8-4.183.80.08614665.0731100
4.18-4.793.80.08314886.6931100
4.79-6.033.80.098147710.2651100
6.03-503.70.082146212.586196.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2VXY

2vxy


Resolution: 2.799→37.446 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.772 / SU ML: 0.36 / σ(F): 1.39 / Phase error: 29.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2429 1055 7.22 %random
Rwork0.2001 ---
obs0.2036 14618 99.53 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 125.53 Å2 / Biso mean: 76.0253 Å2 / Biso min: 33.94 Å2
Refinement stepCycle: LAST / Resolution: 2.799→37.446 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4376 0 56 0 4432
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054470
X-RAY DIFFRACTIONf_angle_d0.9566048
X-RAY DIFFRACTIONf_chiral_restr0.061724
X-RAY DIFFRACTIONf_plane_restr0.003798
X-RAY DIFFRACTIONf_dihedral_angle_d17.4351640
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7992-2.92660.36921190.30981687180699
2.9266-3.08080.3781240.286516971821100
3.0808-3.27370.34231400.284516781818100
3.2737-3.52630.26371440.234417001844100
3.5263-3.88090.28831420.21316801822100
3.8809-4.44170.24141250.195217221847100
4.4417-5.5930.20231320.183817131845100
5.593-37.44890.19781290.15841686181597

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