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- PDB-4dxd: Staphylococcal Aureus FtsZ in complex with 723 -

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Basic information

Entry
Database: PDB / ID: 4dxd
TitleStaphylococcal Aureus FtsZ in complex with 723
ComponentsCell division protein FtsZ
KeywordsCELL CYCLE/INHIBITOR / Rossmann Fold / GTPase / GTP binding / CELL CYCLE-INHIBITOR complex
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
Chem-9PC / GUANOSINE-5'-DIPHOSPHATE / Cell division protein FtsZ
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsLu, J. / Soisson, S.M.
CitationJournal: Sci Transl Med / Year: 2012
Title: Restoring methicillin-resistant Staphylococcus aureus susceptibility to beta-lactam antibiotics.
Authors: Tan, C.M. / Therien, A.G. / Lu, J. / Lee, S.H. / Caron, A. / Gill, C.J. / Lebeau-Jacob, C. / Benton-Perdomo, L. / Monteiro, J.M. / Pereira, P.M. / Elsen, N.L. / Wu, J. / Deschamps, K. / ...Authors: Tan, C.M. / Therien, A.G. / Lu, J. / Lee, S.H. / Caron, A. / Gill, C.J. / Lebeau-Jacob, C. / Benton-Perdomo, L. / Monteiro, J.M. / Pereira, P.M. / Elsen, N.L. / Wu, J. / Deschamps, K. / Petcu, M. / Wong, S. / Daigneault, E. / Kramer, S. / Liang, L. / Maxwell, E. / Claveau, D. / Vaillancourt, J. / Skorey, K. / Tam, J. / Wang, H. / Meredith, T.C. / Sillaots, S. / Wang-Jarantow, L. / Ramtohul, Y. / Langlois, E. / Landry, F. / Reid, J.C. / Parthasarathy, G. / Sharma, S. / Baryshnikova, A. / Lumb, K.J. / Pinho, M.G. / Soisson, S.M. / Roemer, T.
History
DepositionFeb 27, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,7073
Polymers41,9081
Non-polymers7992
Water1,36976
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.715, 54.650, 84.496
Angle α, β, γ (deg.)90.00, 106.75, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Cell division protein FtsZ /


Mass: 41907.684 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: ftsZ / Production host: Escherichia coli (E. coli) / References: UniProt: P0A031
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine 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-9PC / 3-[(6-chloro[1,3]thiazolo[5,4-b]pyridin-2-yl)methoxy]-2,6-difluorobenzamide / PC190723


Mass: 355.747 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H8ClF2N3O2S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 1.79 Å3/Da / Density % sol: 31.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8.5
Details: 0.1M ammonium sulfate, 0.1M TRIS pH8.5 and 25% PEG3350, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Aug 5, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.01→40.46 Å / Num. all: 20207 / Num. obs: 19629 / % possible obs: 97.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
BUSTER-TNTBUSTER 2.9.7refinement
PDB_EXTRACT3.1data extraction
XDSdata scaling
PHASERphasing
BUSTER2.9.7refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.01→40.46 Å / Cor.coef. Fo:Fc: 0.9456 / Cor.coef. Fo:Fc free: 0.9291 / Occupancy max: 1 / Occupancy min: 0.5 / SU R Cruickshank DPI: 0.176 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2216 999 5.1 %RANDOM
Rwork0.1875 ---
all0.1892 20207 --
obs0.1892 19599 98.8 %-
Displacement parametersBiso max: 108.36 Å2 / Biso mean: 37.0147 Å2 / Biso min: 19.02 Å2
Baniso -1Baniso -2Baniso -3
1-3.8965 Å20 Å25.4407 Å2
2---5.6809 Å20 Å2
3---1.7844 Å2
Refine analyzeLuzzati coordinate error obs: 0.245 Å
Refinement stepCycle: LAST / Resolution: 2.01→40.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2147 0 51 76 2274
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d768SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes59HARMONIC8
X-RAY DIFFRACTIONt_gen_planes329HARMONIC8
X-RAY DIFFRACTIONt_it2230HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion314SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2735SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2230HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg3029HARMONIC21.34
X-RAY DIFFRACTIONt_omega_torsion2.3
X-RAY DIFFRACTIONt_other_torsion18.64
LS refinement shellResolution: 2.01→2.12 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.2614 140 4.93 %
Rwork0.2145 2701 -
all0.2168 2841 -
obs--98.8 %

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