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

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Basic information

Entry
Database: PDB / ID: 3wgm
TitleSTAPHYLOCOCCUS AUREUS FTSZ T7 mutant substituted for GAN bound with GTP, DeltaT7GAN-GTP
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'-TRIPHOSPHATE / Cell division protein FtsZ
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.091 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 / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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.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)83,1546
Polymers82,0602
Non-polymers1,0954
Water73941
1
A: Cell division protein FtsZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5773
Polymers41,0301
Non-polymers5472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cell division protein FtsZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5773
Polymers41,0301
Non-polymers5472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.530, 89.640, 66.580
Angle α, β, γ (deg.)90.000, 96.110, 90.000
Int Tables number4
Space group name H-MP1211

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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-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / Source method: isolated from a natural source / Formula: H2O
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: 1.61 Å3/Da / Density % sol: 23.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1M Sodium HEPES, 27.5%(w/v) PEG2000MME, 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: Apr 10, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.09→50 Å / Num. obs: 30298 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 28.75 Å2 / Rmerge(I) obs: 0.118 / Net I/σ(I): 8.13
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
2.09-2.220.6660.7781.9817859497247290.90595.1
2.22-2.370.810.522.9717738464145820.60498.7
2.37-2.560.8970.3634.116629434643010.42299
2.56-2.80.9480.2455.715346399439640.28599.2
2.8-3.130.9750.1568.3513826360435770.18299.3
3.13-3.610.9890.09312.7412198320231730.10999.1
3.61-4.420.9930.06617.6210167271426850.07798.9
4.42-6.220.9930.06219.27890211620940.07399
6.220.9950.05421.114355120711930.06398.8

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
XDSdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3voa

3voa


Resolution: 2.091→44.82 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8519 / SU ML: 0.21 / σ(F): 2.01 / Phase error: 22.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2267 1515 5 %random
Rwork0.1931 ---
obs0.1947 30293 98.39 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 78.39 Å2 / Biso mean: 22.8028 Å2 / Biso min: 2.89 Å2
Refinement stepCycle: LAST / Resolution: 2.091→44.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4330 0 66 41 4437
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054428
X-RAY DIFFRACTIONf_angle_d1.0235994
X-RAY DIFFRACTIONf_chiral_restr0.065718
X-RAY DIFFRACTIONf_plane_restr0.003788
X-RAY DIFFRACTIONf_dihedral_angle_d18.2531630
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0915-2.1590.29841280.2762437256592
2.159-2.23610.27511390.24222645278499
2.2361-2.32560.24751370.21892598273599
2.3256-2.43150.26821370.21932615275299
2.4315-2.55970.25191390.20822631277099
2.5597-2.720.28031380.21022621275999
2.72-2.930.2241390.20152638277799
2.93-3.22480.27391380.20022630276899
3.2248-3.69120.21381390.18362642278199
3.6912-4.64980.19821390.16192629276899
4.6498-44.83030.18281420.17422692283499

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