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- PDB-3fyr: Crystal structure of the sporulation histidine kinase inhibitor S... -

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Basic information

Entry
Database: PDB / ID: 3fyr
TitleCrystal structure of the sporulation histidine kinase inhibitor Sda from Bacillus subtilis
ComponentsSporulation inhibitor sda
KeywordsTransferase inhibitor / helical hairpin / histidine kinase inhibitor / sporulation regulation / Alternative initiation / Protein kinase inhibitor / Sporulation
Function / homologySporulation inhibitor A / Sporulation inhibitor A superfamily / Sporulation inhibitor A / sporulation resulting in formation of a cellular spore / protein kinase inhibitor activity / Sporulation inhibitor sda
Function and homology information
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.97 Å
AuthorsJacques, D.A. / Streamer, M. / King, G.F. / Guss, J.M. / Trewhella, J. / Langley, D.B.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2009
Title: Structure of the sporulation histidine kinase inhibitor Sda from Bacillus subtilis and insights into its solution state
Authors: Jacques, D.A. / Streamer, M. / Rowland, S.L. / King, G.F. / Guss, J.M. / Trewhella, J. / Langley, D.B.
History
DepositionJan 23, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 23, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sporulation inhibitor sda
B: Sporulation inhibitor sda
C: Sporulation inhibitor sda


Theoretical massNumber of molelcules
Total (without water)17,0593
Polymers17,0593
Non-polymers00
Water1448
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2270 Å2
ΔGint-22 kcal/mol
Surface area6430 Å2
MethodPISA
2
A: Sporulation inhibitor sda
B: Sporulation inhibitor sda
C: Sporulation inhibitor sda

A: Sporulation inhibitor sda
B: Sporulation inhibitor sda
C: Sporulation inhibitor sda


Theoretical massNumber of molelcules
Total (without water)34,1176
Polymers34,1176
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area6360 Å2
ΔGint-65 kcal/mol
Surface area11030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.972, 36.972, 167.173
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
DetailsTHE DEPOSITORS HAVE IN DEPENDANT DATA WHICH SUGGESTS THAT IN SOLUTION THE OLIGOMERIC STATE OF THE ASU (IE AN ODD-LOOKING TRIMER) BEST FITS SAXS DATA OF THE PROTEIN IN SOLUTION.

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Components

#1: Protein/peptide Sporulation inhibitor sda / sda / Histidine kinase kinA inhibitor


Mass: 5686.198 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: subtilis str. 168 / Gene: BSU25690, sda / Plasmid: pSLR65 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 (DE3) / References: UniProt: Q7WY62
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE FIRST 6 RESIDUES, MNWVPS, ARE MISSING IN NATURAL ACCORDING TO REFERENCE 2, SDA_BACSU IN UNIPROT. ...THE FIRST 6 RESIDUES, MNWVPS, ARE MISSING IN NATURAL ACCORDING TO REFERENCE 2, SDA_BACSU IN UNIPROT. THERE IS AN ALTERNATE START CODON WHICH THE DEPOSITORS BELIEVE IS SELDOM USED, HENCE THE NUMBERING THEY HAVE EMPLOYED.

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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: 1.718006 Å3/Da / Density % sol: 28.405363 % / Mosaicity: 0.639 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.3
Details: equal volumes of protein solution (7.5 mg/ml) and well solution (0.1M MES, pH 6.3, 15% (w/v) PEG 5000MME) were combined., VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97945, 0.97959, 0.94945
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 20, 2008
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979451
20.979591
30.949451
ReflectionRedundancy: 3.6 % / Av σ(I) over netI: 14.87 / Number: 56720 / Rmerge(I) obs: 0.06 / Χ2: 1 / D res high: 1.97 Å / D res low: 50 Å / Num. obs: 15638 / % possible obs: 99.5
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
1.972.0499.910.5641.0293.1
2.042.1299.910.4151.0183.7
2.122.2299.910.2931.0243.6
2.222.3499.810.2020.9993.6
2.342.4899.910.1321.0093.5
2.482.6799.810.10.9823.5
2.672.9499.510.0750.9833.5
2.943.3799.210.0540.9993.5
3.374.2498.810.0490.9343.7
4.245098.410.0351.0564.6
ReflectionResolution: 1.97→50 Å / Num. obs: 8936 / % possible obs: 99.5 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.06 / Χ2: 1.005 / Net I/σ(I): 14.873
Reflection shellResolution: 1.97→2.04 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.564 / Mean I/σ(I) obs: 2 / Num. unique all: 1577 / Χ2: 1.029 / % possible all: 99.9

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Phasing

PhasingMethod: MAD
Phasing set
ID
1
2
3
Phasing MAD set
Clust-IDExpt-IDSet-IDWavelength (Å)F double prime refinedF prime refined
13 wavelength10.97946.18-7.71
13 wavelength20.97963.68-9.86
13 wavelength30.94953.32-4.15
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se23.9340.7530.5810.0420.622
2Se50.4150.3460.8950.0210.37
3Se56.1150.0360.6340.0650.488

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.1phasing
RESOLVEphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
RefinementMethod to determine structure: MAD / Resolution: 1.97→27.69 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.879 / WRfactor Rfree: 0.325 / WRfactor Rwork: 0.265 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.796 / SU B: 4.771 / SU ML: 0.136 / SU R Cruickshank DPI: 0.201 / SU Rfree: 0.198 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.201 / ESU R Free: 0.198 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.304 420 4.7 %RANDOM
Rwork0.234 ---
obs0.238 8860 99.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 77.98 Å2 / Biso mean: 37.902 Å2 / Biso min: 21.37 Å2
Baniso -1Baniso -2Baniso -3
1-0.69 Å20 Å20 Å2
2--0.69 Å20 Å2
3----1.38 Å2
Refinement stepCycle: LAST / Resolution: 1.97→27.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms880 0 0 8 888
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.022887
X-RAY DIFFRACTIONr_bond_other_d0.0010.02596
X-RAY DIFFRACTIONr_angle_refined_deg1.0741.9861190
X-RAY DIFFRACTIONr_angle_other_deg0.86631448
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.155111
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.58423.33339
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.84815163
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.248158
X-RAY DIFFRACTIONr_chiral_restr0.0580.2143
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02973
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02187
X-RAY DIFFRACTIONr_mcbond_it2.0412566
X-RAY DIFFRACTIONr_mcbond_other0.6012226
X-RAY DIFFRACTIONr_mcangle_it3.2823889
X-RAY DIFFRACTIONr_scbond_it5.0524321
X-RAY DIFFRACTIONr_scangle_it7.6996301
LS refinement shellResolution: 1.971→2.022 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 31 -
Rwork0.294 596 -
all-627 -
obs--99.52 %

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