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- PDB-4jgr: The crystal structure of sporulation kinase D mutant sensor domai... -

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Basic information

Entry
Database: PDB / ID: 4jgr
TitleThe crystal structure of sporulation kinase D mutant sensor domain, R131A, from Bacillus subtilis subsp at 2.4A resolution
ComponentsSporulation kinase D
KeywordsTRANSFERASE / PAS-like fold / Histidine kinase / Extracytoplasmic / alpha-beta-alpha structure / Structural Genomics / Midwest Center for Structural Genomics / MCSG / PSI-Biology
Function / homology
Function and homology information


sporulation resulting in formation of a cellular spore / histidine kinase / phosphorelay sensor kinase activity / ATP binding / plasma membrane
Similarity search - Function
Double Cache domain 1 / Cache domain / Periplasmic sensor-like domain superfamily / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / PAS domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Signal transduction histidine kinase-related protein, C-terminal / Histidine kinase domain ...Double Cache domain 1 / Cache domain / Periplasmic sensor-like domain superfamily / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / PAS domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Signal transduction histidine kinase-related protein, C-terminal / Histidine kinase domain / Histidine kinase domain profile. / Beta-Lactamase / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / Sporulation kinase D
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsWu, R. / Schiffer, M. / Gu, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: Protein Sci. / Year: 2013
Title: Insight into the sporulation phosphorelay: Crystal structure of the sensor domain of Bacillus subtilis histidine kinase, KinD.
Authors: Wu, R. / Gu, M. / Wilton, R. / Babnigg, G. / Kim, Y. / Pokkuluri, P.R. / Szurmant, H. / Joachimiak, A. / Schiffer, M.
History
DepositionMar 1, 2013Deposition site: RCSB / Processing site: RCSB
SupersessionMay 15, 2013ID: 4DBI
Revision 1.0May 15, 2013Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sporulation kinase D
B: Sporulation kinase D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,3777
Polymers48,9802
Non-polymers3965
Water3,153175
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2530 Å2
ΔGint-10 kcal/mol
Surface area20270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.663, 83.424, 91.006
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 Sporulation kinase D / Sensor histidine kinase D


Mass: 24490.166 Da / Num. of mol.: 2 / Fragment: SENSOR DOMAIN (UNP RESIDUES 37-250) / Mutation: R95A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis (bacteria)
Strain: 168 / Gene: BSU13660, kinD, ykvD / Plasmid: PMCSG7 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 MAGIC / References: UniProt: O31671, histidine kinase
#2: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / 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: 2.97 Å3/Da / Density % sol: 58.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2M AMMONIUM ACETATE, 0.1M BIS-TRIS AND 25% (W/V) PEG3350, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97903
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 20, 2011 / Details: MIRRORS
RadiationMonochromator: SI 111, CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97903 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 23104 / % possible obs: 99.2 % / Observed criterion σ(I): 0 / Redundancy: 9.5 % / Biso Wilson estimate: 50 Å2 / Rsym value: 0.088 / Net I/σ(I): 29.6
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 9.6 % / Mean I/σ(I) obs: 4.6 / Rsym value: 0.61 / % possible all: 99.7

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Processing

Software
NameVersionClassification
MLPHAREphasing
PHENIX(PHENIX.REFINE: 1.7.1_743)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.4→37.92 Å / SU ML: 0.97 / σ(F): 1.34 / Phase error: 24.7 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.252 2244 5.13 %
Rwork0.201 --
obs0.204 43719 99.1 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.49 Å2 / ksol: 0.33 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.0524 Å20 Å2-0 Å2
2--6.5757 Å20 Å2
3----7.6282 Å2
Refinement stepCycle: LAST / Resolution: 2.4→37.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3198 0 26 175 3399
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083278
X-RAY DIFFRACTIONf_angle_d1.0974435
X-RAY DIFFRACTIONf_dihedral_angle_d16.9171228
X-RAY DIFFRACTIONf_chiral_restr0.077525
X-RAY DIFFRACTIONf_plane_restr0.004558
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.3996-2.45180.31891620.292501266397
2.4518-2.50880.34171380.28262615275399
2.5088-2.57150.32461440.28222580272499
2.5715-2.6410.3661320.27372598273099
2.641-2.71870.36891550.24462561271699
2.7187-2.80650.29861370.23372589272699
2.8065-2.90670.32521250.22822655278099
2.9067-3.02310.32741190.22312564268399
3.0231-3.16060.27481520.20272595274799
3.1606-3.32710.24821270.203626202747100
3.3271-3.53540.26941560.212126062762100
3.5354-3.80820.25651570.204725912748100
3.8082-4.1910.2191230.18126222745100
4.191-4.79640.16681180.138826262744100
4.7964-6.0390.20591530.162626022755100
6.039-37.92350.21671460.20422550269698
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.33542.10980.97242.58010.89492.32690.1245-0.076-0.09720.05160.00430.0316-0.18480.1635-0.06080.2005-0.0032-0.04340.1756-0.01140.194473.52263.581-21.231
21.40580.45180.22262.39330.42610.8187-0.27340.3312-0.006-0.74540.4422-0.2366-0.28990.7916-0.08760.2852-0.18920.0170.4381-0.08740.201457.02679.319-24.72
32.17451.47430.09192.25890.20981.7321-0.0370.0573-0.23550.0562-0.0003-0.0011-0.11820.21550.02430.1542-0.04140.01830.2346-0.00330.171672.25864.8042.598
42.45741.8194-0.40442.62740.1281.74020.14410.04870.1137-0.0755-0.03130.152-0.2824-0.0442-0.0960.2514-0.0407-0.02770.21270.0350.167261.66983.7995.899
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 41:181 )
2X-RAY DIFFRACTION2(CHAIN A AND RESID 182:243 )
3X-RAY DIFFRACTION3(CHAIN B AND RESID 38:181 )
4X-RAY DIFFRACTION4(CHAIN B AND RESID 182:243 )

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