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- PDB-3wgl: STAPHYLOCOCCUS AUREUS FTSZ T7 mutant substituted for GAN bound wi... -

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Basic information

Entry
Database: PDB / ID: 3wgl
TitleSTAPHYLOCOCCUS AUREUS FTSZ T7 mutant substituted for GAN bound with GDP, DeltaT7GAN-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: 3.066 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 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_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_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)82,9464
Polymers82,0602
Non-polymers8862
Water00
1
A: Cell division protein FtsZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4732
Polymers41,0301
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)41,4732
Polymers41,0301
Non-polymers4431
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.886, 97.156, 72.559
Angle α, β, γ (deg.)90.000, 102.410, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain: (Details: CHAIN B) / NCS domain segments: (Selection details: CHAIN B)

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Components

#1: Protein Cell division protein FtsZ


Mass: 41029.762 Da / Num. of mol.: 2 / Mutation: 204SGEV207 to GA
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 204-207 (SGEV) WERE REPLACED WITH GA.

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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: 1.88 Å3/Da / Density % sol: 34.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1M Sodium HEPES, 30%(w/v) PEG2000MME, vapor diffusion, sitting drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Dec 16, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 3.066→50 Å / Num. obs: 11397 / % possible obs: 99 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 62.64 Å2 / Rmerge(I) obs: 0.151 / Net I/σ(I): 10.22
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
3.07-3.250.6760.7551.96259185218130.89497.9
3.25-3.470.8360.4473.45591174417150.53798.3
3.47-3.750.9120.2916.155489160115910.34499.4
3.75-4.110.9630.1859.365093148814870.21999.9
4.11-4.590.9820.11513.724668135313470.13699.6
4.59-5.290.9880.08915.834016118411790.10699.6
5.29-6.460.9890.09415.133492103710320.11299.5
6.46-9.050.9960.05321.8825707887790.06398.9
9.050.9970.03630.2114334634540.04398.1

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
XDSdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WGK

3wgk


Resolution: 3.066→48.578 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8059 / SU ML: 0.42 / σ(F): 1.37 / Phase error: 26.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.265 542 4.76 %random
Rwork0.2091 ---
obs0.2117 11391 99.03 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 105.89 Å2 / Biso mean: 42.1279 Å2 / Biso min: 13.9 Å2
Refinement stepCycle: LAST / Resolution: 3.066→48.578 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4376 0 56 0 4432
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044469
X-RAY DIFFRACTIONf_angle_d0.9116047
X-RAY DIFFRACTIONf_chiral_restr0.034725
X-RAY DIFFRACTIONf_plane_restr0.005797
X-RAY DIFFRACTIONf_dihedral_angle_d19.8121640
Refine LS restraints NCSNumber: 2563 / Type: POSITIONAL / Rms dev position: 16.949 Å
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 (%)
3.0656-3.3740.34711400.29582654279498
3.374-3.8620.29261410.232699284099
3.862-4.8650.2161340.185727462880100
4.865-48.58410.2551270.18672750287799

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