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- PDB-5h5h: Staphylococcus aureus FtsZ-GDP R29A mutant in T state -

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Basic information

Entry
Database: PDB / ID: 5h5h
TitleStaphylococcus aureus FtsZ-GDP R29A mutant in T state
ComponentsCell division protein FtsZ
KeywordsCELL CYCLE / Tubulin/FtsZ family / GTPase / protofilament
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'-DIPHOSPHATE / Cell division protein FtsZ
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsFujita, J. / Harada, R. / Maeda, Y. / Saito, Y. / Mizohata, E. / Inoue, T. / Shigeta, Y. / Matsumura, H.
Funding support Japan, 9items
OrganizationGrant numberCountry
The Japan Society for the Promotion of Science15J00589 Japan
The Japan Society for the Promotion of Science26102526 Japan
The Japan Society for the Promotion of Science16H00783 Japan
The Japan Society for the Promotion of Science15J03797 Japan
The Japan Society for the Promotion of Science16H06164 Japan
The Japan Society for the Promotion of Science26107004 Japan
The Japan Society for the Promotion of Science26105012 Japan
The Japan Society for the Promotion of Science24109017 Japan
The Japan Society for the Promotion of Science15H04443 Japan
CitationJournal: J. Struct. Biol. / Year: 2017
Title: Identification of the key interactions in structural transition pathway of FtsZ from Staphylococcus aureus
Authors: Fujita, J. / Harada, R. / Maeda, Y. / Saito, Y. / Mizohata, E. / Inoue, T. / Shigeta, Y. / Matsumura, H.
History
DepositionNov 5, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 24, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 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
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_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_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.pdbx_ptnr2_label_alt_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.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_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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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)32,2503
Polymers31,7671
Non-polymers4832
Water4,342241
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area820 Å2
ΔGint-15 kcal/mol
Surface area13340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.525, 50.834, 88.477
Angle α, β, γ (deg.)90.000, 110.630, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-673-

HOH

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Components

#1: Protein Cell division protein FtsZ


Mass: 31766.908 Da / Num. of mol.: 1 / Fragment: UNP residues 12-316 / Mutation: R29A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (strain MRSA252) (bacteria)
Strain: MRSA252 / Gene: ftsZ, SAR1162 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6GHP9
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 241 / 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: 48.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.1 / Details: 100mM Tris, 43% w/v PEP629, 300mM KCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Apr 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 32530 / % possible obs: 99.5 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.13 / Net I/av σ(I): 14.316 / Net I/σ(I): 4.9
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.7-1.734.10.9615930.6110.5491.1080.318100
1.73-1.764.20.81116300.7750.460.9340.257100
1.76-1.794.10.72616140.7630.4140.8380.278100
1.79-1.834.20.6216470.8630.3510.7130.338100
1.83-1.874.10.55816110.830.3180.6430.369100
1.87-1.914.10.64616250.3740.380.7510.679100
1.91-1.964.10.56216330.5880.3240.650.682100
1.96-2.024.20.28116330.9480.1580.3230.51100
2.02-2.074.10.34516340.7470.2030.4020.81399.9
2.07-2.1440.27216080.9120.160.3170.87499.9
2.14-2.224.20.19516410.9710.110.2240.798100
2.22-2.3140.25516480.840.1520.2981.39199.9
2.31-2.414.10.15616130.980.0880.181.043100
2.41-2.544.10.14616400.9570.0830.1681.2899.9
2.54-2.74.10.13916280.9790.0790.161.52899.8
2.7-2.914.10.11616470.9850.0650.1331.75399.9
2.91-3.24.10.116270.9880.0560.1151.96799.4
3.2-3.6640.0916390.990.0510.1032.01998.9
3.66-4.613.90.08616280.9860.0490.0991.96198.4
4.61-503.90.08415910.9860.0490.0971.69693.3

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8.0135refinement
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
PHASERphasing
HKLdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VOA

3voa


Resolution: 1.7→41.4 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.948 / SU B: 2.662 / SU ML: 0.084 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.109 / ESU R Free: 0.112
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.226 1611 5 %RANDOM
Rwork0.1818 ---
obs0.184 30919 98.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 82.97 Å2 / Biso mean: 27.585 Å2 / Biso min: 10.81 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å2-0.01 Å2
2--0.02 Å20 Å2
3---0.01 Å2
Refinement stepCycle: final / Resolution: 1.7→41.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2195 0 29 244 2468
Biso mean--18.51 35.04 -
Num. residues----305
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0192283
X-RAY DIFFRACTIONr_bond_other_d0.0020.022239
X-RAY DIFFRACTIONr_angle_refined_deg1.7071.9833100
X-RAY DIFFRACTIONr_angle_other_deg0.97735161
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8975318
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.72526.92391
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.48215401
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.996159
X-RAY DIFFRACTIONr_chiral_restr0.0970.2372
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022662
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02457
X-RAY DIFFRACTIONr_mcbond_it2.0252.4561233
X-RAY DIFFRACTIONr_mcbond_other2.0212.4551232
X-RAY DIFFRACTIONr_mcangle_it3.0193.6761543
LS refinement shellResolution: 1.699→1.743 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.234 119 -
Rwork0.258 2062 -
all-2181 -
obs--90.65 %

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