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- PDB-2vxy: The structure of FTsZ from Bacillus subtilis at 1.7A resolution -

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Basic information

Entry
Database: PDB / ID: 2vxy
TitleThe structure of FTsZ from Bacillus subtilis at 1.7A resolution
ComponentsCELL DIVISION PROTEIN FTSZ
KeywordsCELL CYCLE / GTP-BINDING / CELL DIVISION / NUCLEOTIDE-BINDING / FTSZ / SEPTATION / CYTOPLASM / B.SUBTILIS / CELL DIVISION PROTEIN
Function / homology
Function and homology information


cell septum / division septum assembly / FtsZ-dependent cytokinesis / cell division site / protein polymerization / cell division / GTPase activity / GTP binding / identical protein 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
CITRIC ACID / : / Cell division protein FtsZ
Similarity search - Component
Biological speciesBACILLUS SUBTILIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsBarynin, V.V. / Baker, P.J. / Rice, D.W. / Sedelnikova, S.E. / Haydon, D.J. / Stokes, N.R. / Ure, R. / Galbraith, G. / Bennett, J.M. / Brown, D.R. ...Barynin, V.V. / Baker, P.J. / Rice, D.W. / Sedelnikova, S.E. / Haydon, D.J. / Stokes, N.R. / Ure, R. / Galbraith, G. / Bennett, J.M. / Brown, D.R. / Heal, J.R. / Sheridan, J.M. / Aiwale, S.T. / Chauhan, P.K. / Srivastava, A. / Taneja, A. / Collins, I. / Errington, J. / Czaplewski, L.G.
CitationJournal: Science / Year: 2008
Title: An Inhibitor of Ftsz with Potent and Selective Anti-Staphylococcal Activity.
Authors: Haydon, D.J. / Stokes, N.R. / Ure, R. / Galbraith, G. / Bennett, J.M. / Brown, D.R. / Baker, P.J. / Barynin, V.V. / Rice, D.W. / Sedelnikova, S.E. / Heal, J.R. / Sheridan, J.M. / Aiwale, S.T. ...Authors: Haydon, D.J. / Stokes, N.R. / Ure, R. / Galbraith, G. / Bennett, J.M. / Brown, D.R. / Baker, P.J. / Barynin, V.V. / Rice, D.W. / Sedelnikova, S.E. / Heal, J.R. / Sheridan, J.M. / Aiwale, S.T. / Chauhan, P.K. / Srivastava, A. / Taneja, A. / Collins, I. / Errington, J. / Czaplewski, L.G.
History
DepositionJul 15, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 30, 2008Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.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_label_seq_id / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6273
Polymers40,3961
Non-polymers2312
Water5,711317
1
A: CELL DIVISION PROTEIN FTSZ
hetero molecules

A: CELL DIVISION PROTEIN FTSZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,2546
Polymers80,7912
Non-polymers4624
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+2/31
Buried area2920 Å2
ΔGint-18 kcal/mol
Surface area29880 Å2
MethodPQS
Unit cell
Length a, b, c (Å)87.170, 87.170, 89.460
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein CELL DIVISION PROTEIN FTSZ / FTSZ


Mass: 40395.660 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS SUBTILIS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P17865
#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 317 / 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: 2.38 Å3/Da / Density % sol: 48 % / Description: NONE
Crystal growpH: 8 / Details: pH 8.0

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.488
DetectorType: ADSC CCD / Detector: CCD / Date: May 3, 2005 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 1.7→34.77 Å / Num. obs: 43398 / % possible obs: 99.3 % / Observed criterion σ(I): 1 / Redundancy: 6.4 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 14.8
Reflection shellResolution: 1.7→1.73 Å / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 1.9 / % possible all: 86.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FSZ

1fsz


Resolution: 1.7→36 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.957 / SU B: 2.071 / SU ML: 0.068 / Cross valid method: THROUGHOUT / ESU R: 0.093 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. NULL
RfactorNum. reflection% reflectionSelection details
Rfree0.218 2566 5.9 %RANDOM
Rwork0.184 ---
obs0.186 40830 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 34.7 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0.01 Å20 Å2
2---0.02 Å20 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.7→36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2207 0 14 317 2538
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222266
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4611.9813063
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3055305
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.9126.51789
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.56315409
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6991511
X-RAY DIFFRACTIONr_chiral_restr0.1010.2374
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021656
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2390.21119
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3040.21601
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1840.2225
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1660.249
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2070.226
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9881.51506
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.78122409
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.9293762
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.2054.5654
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.73 Å / Total num. of bins used: 30 /
RfactorNum. reflection
Rfree0.311 105
Rwork0.31 1908

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