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- PDB-1nat: CRYSTAL STRUCTURE OF SPOOF FROM BACILLUS SUBTILIS -

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Basic information

Entry
Database: PDB / ID: 1nat
TitleCRYSTAL STRUCTURE OF SPOOF FROM BACILLUS SUBTILIS
ComponentsSPORULATION RESPONSE REGULATORY PROTEIN
KeywordsREGULATORY PROTEIN / ASPARTATE POCKET / SPORULATION RESPONSE REGULATOR / TWO COMPONENT SYSTEM
Function / homology
Function and homology information


Transferases; Transferring phosphorus-containing groups / sporulation resulting in formation of a cellular spore / phosphorelay signal transduction system / kinase activity / phosphorylation / metal ion binding / cytoplasm
Similarity search - Function
Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Response regulator / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Sporulation initiation phosphotransferase F
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsMadhusudan / Zapf, J. / Hoch, J.A. / Whiteley, J.M. / Xuong, N.H. / Varughese, K.I.
CitationJournal: Biochemistry / Year: 1997
Title: A response regulatory protein with the site of phosphorylation blocked by an arginine interaction: crystal structure of Spo0F from Bacillus subtilis.
Authors: Madhusudan, M. / Zapf, J. / Hoch, J.A. / Whiteley, J.M. / Xuong, N.H. / Varughese, K.I.
History
DepositionSep 9, 1997Processing site: BNL
Revision 1.0Oct 14, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SPORULATION RESPONSE REGULATORY PROTEIN


Theoretical massNumber of molelcules
Total (without water)14,2451
Polymers14,2451
Non-polymers00
Water36020
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.500, 58.500, 85.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein SPORULATION RESPONSE REGULATORY PROTEIN / SPO0F


Mass: 14244.660 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: SPO0F / Plasmid: PET20B / Gene (production host): SPO0F / Production host: Escherichia coli (E. coli) / References: UniProt: P06628
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 2.56 Å3/Da / Density % sol: 50 %
Crystal growpH: 7.8 / Details: pH 7.8
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
115 mg/mlprotein1drop
225 %PEG45001reservoir
315 %ethanol1reservoir
4100 mMsodium potassium phosphate1reservoirpH7.8

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Data collection

DiffractionMean temperature: 300 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: Sep 1, 1991
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.45→50 Å / Num. obs: 24763 / % possible obs: 92.7 % / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 19.8
Reflection shellResolution: 2.45→2.64 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.153 / Mean I/σ(I) obs: 4.2 / % possible all: 79.8
Reflection
*PLUS
Num. obs: 5449 / Num. measured all: 24763

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLORrefinement
UCSDdata reduction
SCAL1(UCSD)data scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Starting model: 13 / Resolution: 2.45→8 Å / σ(F): 2
RfactorNum. reflection% reflection
Rwork0.181 --
obs0.181 5449 92.7 %
Displacement parametersBiso mean: 38 Å2
Baniso -1Baniso -2Baniso -3
1-2.14 Å20 Å20 Å2
2--2.14 Å20 Å2
3----4.28 Å2
Refinement stepCycle: LAST / Resolution: 2.45→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms944 0 2 20 966
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.017
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_deg1.8
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
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 4935 / Rfactor obs: 0.176
Solvent computation
*PLUS
Displacement parameters
*PLUS

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