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- PDB-1ixm: CRYSTAL STRUCTURE OF SPOOB FROM BACILLUS SUBTILIS -

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Basic information

Entry
Database: PDB / ID: 1ixm
TitleCRYSTAL STRUCTURE OF SPOOB FROM BACILLUS SUBTILIS
ComponentsPROTEIN (SPORULATION RESPONSE REGULATORY PROTEIN)
KeywordsTRANSFERASE / PHOSPHOTRANSFERASE / SPORULATION RESPONSE REGULATOR / TWO COMPONENT SYSTEM / REGULATORY PROTEIN
Function / homology
Function and homology information


Transferases; Transferring phosphorus-containing groups / sporulation resulting in formation of a cellular spore / phosphorelay sensor kinase activity / cytoplasm
Similarity search - Function
Sporulation initiation phosphotransferase B (SpoOB), C-terminal domain / Sporulation initiation phosphotransferase B, C-terminal / Sporulation initiation phosphotransferase B, C-terminal domain superfamily / Sporulation initiation phospho-transferase B, C-terminal / Sporulation initiation phospho-transferase B, C-terminal / SpoOB, alpha-helical domain / Sensor_kinase_SpoOB-type, alpha-helical domain / Signal transduction histidine kinase, sporulation regulator SpoOB / Signal transduction histidine kinase, dimerisation/phosphotransfer (DHp) domain / Heat Shock Protein 90 ...Sporulation initiation phosphotransferase B (SpoOB), C-terminal domain / Sporulation initiation phosphotransferase B, C-terminal / Sporulation initiation phosphotransferase B, C-terminal domain superfamily / Sporulation initiation phospho-transferase B, C-terminal / Sporulation initiation phospho-transferase B, C-terminal / SpoOB, alpha-helical domain / Sensor_kinase_SpoOB-type, alpha-helical domain / Signal transduction histidine kinase, sporulation regulator SpoOB / Signal transduction histidine kinase, dimerisation/phosphotransfer (DHp) domain / Heat Shock Protein 90 / Helix Hairpins / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Sporulation initiation phosphotransferase B
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.6 Å
AuthorsVarughese, K.I.
CitationJournal: Mol.Cell / Year: 1998
Title: Formation of a novel four-helix bundle and molecular recognition sites by dimerization of a response regulator phosphotransferase.
Authors: Varughese, K.I. / Madhusudan / Zhou, X.Z. / Whiteley, J.M. / Hoch, J.A.
History
DepositionNov 6, 1998Processing site: RCSB
Revision 1.0Nov 25, 1998Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (SPORULATION RESPONSE REGULATORY PROTEIN)
B: PROTEIN (SPORULATION RESPONSE REGULATORY PROTEIN)


Theoretical massNumber of molelcules
Total (without water)45,1472
Polymers45,1472
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3240 Å2
ΔGint-40 kcal/mol
Surface area16480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.400, 94.400, 109.700
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 PROTEIN (SPORULATION RESPONSE REGULATORY PROTEIN) / SPO0B


Mass: 22573.559 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Description: BACTERIOPHAGE T7 PROMOTER / Gene: SPO0B / Plasmid: PET20B / Gene (production host): SPO0B / Production host: Bacillus subtilis (bacteria) / References: UniProt: P06535

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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: 2.5 Å3/Da / Density % sol: 51.68 %
Crystal growpH: 8.5 / Details: 2M AMMONIUM SULPHATE PH 8.5
Crystal
*PLUS
Density % sol: 50 %
Crystal grow
*PLUS
Temperature: 295 K / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
176 mg/mlprotein1drop
22 Mammonium sulfate1reservoir
3100 mMTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 1, 1997 / Details: MIRROR
RadiationMonochromator: CHARLES SUPPER MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 14203 / % possible obs: 96.6 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Rsym value: 0.08 / Net I/σ(I): 17.6
Reflection shellResolution: 2.6→2.72 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 2.4 / Rsym value: 0.225 / % possible all: 92.3
Reflection
*PLUS
Num. measured all: 42324 / Rmerge(I) obs: 0.08
Reflection shell
*PLUS
% possible obs: 92.3 % / Rmerge(I) obs: 0.225

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Processing

Software
NameClassification
PHASESphasing
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIR / Resolution: 2.6→35 Å / Isotropic thermal model: UNRESTRAINED / Cross valid method: THROUGHTOUT / σ(F): 2 / Details: OTHER REFINEMENT PROGRAM USED: NULL
RfactorNum. reflection% reflectionSelection details
Rfree0.314 1320 10 %RANDOM
Rwork0.217 ---
obs-13201 89.2 %-
Displacement parametersBiso mean: 36.8 Å2
Refine analyzeLuzzati d res low obs: 35 Å
Refinement stepCycle: LAST / Resolution: 2.6→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2489 0 0 0 2489
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.8
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.6→2.72 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.42 125 10.2 %
Rwork0.32 1094 -
obs--66 %
Xplor fileSerial no: 1 / Param file: PARAM19X.PRO / Topol file: TOPH19X.PRO

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