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- PDB-1ofu: Crystal structure of SulA:FtsZ from Pseudomonas aeruginosa -

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Basic information

Entry
Database: PDB / ID: 1ofu
TitleCrystal structure of SulA:FtsZ from Pseudomonas aeruginosa
Components
  • CELL DIVISION PROTEIN FTSZ
  • HYPOTHETICAL PROTEIN PA3008
KeywordsBACTERIAL CELL DIVISION INHIBITOR / FTSZ / SULA PROTEIN
Function / homology
Function and homology information


negative regulation of cell division / division septum assembly / FtsZ-dependent cytokinesis / SOS response / cell division site / protein polymerization / cell division / DNA repair / GTPase activity / GTP binding / cytoplasm
Similarity search - Function
Cell division suppressor protein, SulA / : / Cell division inhibitor SulA / 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 ...Cell division suppressor protein, SulA / : / Cell division inhibitor SulA / 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 / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Cell division protein FtsZ / Cell division inhibitor SulA
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsCordell, S.C. / Robinson, E.J.H. / Lowe, J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2003
Title: Crystal Structure of the SOS Cell Division Inhibitor Sula and in Complex with Ftsz
Authors: Cordell, S.C. / Robinson, E.J.H. / Lowe, J.
History
DepositionApr 21, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 19, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 1, 2024Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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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
X: HYPOTHETICAL PROTEIN PA3008
Y: HYPOTHETICAL PROTEIN PA3008
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,2266
Polymers92,3404
Non-polymers8862
Water7,945441
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)55.590, 75.410, 241.040
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein CELL DIVISION PROTEIN FTSZ / FTSZ


Mass: 33146.961 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-320
Source method: isolated from a genetically manipulated source
Details: LAST 75 RESIDUES REMOVED FROM C-TERMINUS / Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Plasmid: PHIS17 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P47204
#2: Protein HYPOTHETICAL PROTEIN PA3008 / SULA


Mass: 13023.056 Da / Num. of mol.: 2 / Fragment: RESIDUES 43-161
Source method: isolated from a genetically manipulated source
Details: FIRST 42 RESIDUES REMOVED FROM N-TERMINUS / Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Plasmid: PHIS17 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q9HZJ8
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 441 / 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: 2.74 Å3/Da / Density % sol: 55.04 %
Crystal growpH: 5.6 / Details: pH 5.60
Crystal grow
*PLUS
Temperature: 19 ℃ / pH: 7.5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
1200 mM1dropNaCl
220 mMTris1drop
35 mMdithiothreitol1drop
45 mM1dropMgCl2
50.1 mMGTP1drop
61 mM1dropNaN3pH7.5
77.5 %PEG200001reservoir
87.5 %PEG550 MME1reservoir
980 mMsodium formate1reservoir
100.1 MTris1reservoirpH7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393
DetectorDetector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9393 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 60044 / % possible obs: 99.7 % / Redundancy: 3.7 % / Biso Wilson estimate: 34.8 Å2 / Rmerge(I) obs: 0.096 / Net I/σ(I): 11.4
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.334 / Mean I/σ(I) obs: 3.7 / % possible all: 99.7
Reflection
*PLUS
Highest resolution: 2.1 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.096
Reflection shell
*PLUS
% possible obs: 99.7 % / Rmerge(I) obs: 0.334 / Mean I/σ(I) obs: 3.7

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: MAD MODEL FROM C2 CRYSTAL FORM

Resolution: 2.1→50 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2554 3011 5 %RANDOM
Rwork0.2159 ---
obs0.2159 60260 99.6 %-
Displacement parametersBiso mean: 43.7 Å2
Baniso -1Baniso -2Baniso -3
1-6.82 Å20 Å20 Å2
2---19.056 Å20 Å2
3---12.236 Å2
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6244 0 56 441 6741
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.261
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: RESTRAINTS
LS refinement shellResolution: 2.1→2.11 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.405 47 5 %
Rwork0.3536 1117 -
Refinement
*PLUS
Rfactor Rfree: 0.255 / Rfactor Rwork: 0.216
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Rfactor Rfree: 0.405 / Rfactor Rwork: 0.354

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