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- PDB-4jgp: The crystal structure of sporulation kinase D sensor domain from ... -

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Basic information

Entry
Database: PDB / ID: 4jgp
TitleThe crystal structure of sporulation kinase D sensor domain from Bacillus subtilis subsp in complex with pyruvate at 2.0A 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 / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / PAS domain / 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 / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / PAS domain / 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
PYRUVIC ACID / Sporulation kinase D
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.03 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: 4DAH
Revision 1.0May 15, 2013Provider: repository / Type: Initial release
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)49,3294
Polymers49,1532
Non-polymers1762
Water5,368298
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2410 Å2
ΔGint-1 kcal/mol
Surface area20560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.374, 82.151, 90.678
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: 24576.283 Da / Num. of mol.: 2 / Fragment: Sensor domain (UNP residues 37-250)
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-PYR / PYRUVIC ACID / Pyruvic acid


Mass: 88.062 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H4O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 298 / 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: 2.89 Å3/Da / Density % sol: 57.49 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M AMMONIUM SULFATE, 0.1 M SODIUM CACODYLATE:HCL AND 30% (W/V) PEG 8000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97924
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: 0.97924 Å / Relative weight: 1
ReflectionResolution: 2.03→50 Å / Num. obs: 36578 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 7.9 % / Biso Wilson estimate: 23.8 Å2 / Rsym value: 0.063 / Net I/σ(I): 33.1
Reflection shellResolution: 2.03→2.07 Å / Redundancy: 7.9 % / Mean I/σ(I) obs: 4.9 / Rsym value: 0.638 / % possible all: 100

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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: 2.03→37.42 Å / SU ML: 0.49 / σ(F): 1.34 / Phase error: 20.75 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.216 3161 5.01 %
Rwork0.179 --
obs0.181 63152 88.9 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.17 Å2 / ksol: 0.34 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.0188 Å2-0 Å20 Å2
2---1.6011 Å2-0 Å2
3---0.5823 Å2
Refinement stepCycle: LAST / Resolution: 2.03→37.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3242 0 12 298 3552
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073406
X-RAY DIFFRACTIONf_angle_d1.0434609
X-RAY DIFFRACTIONf_dihedral_angle_d14.8921293
X-RAY DIFFRACTIONf_chiral_restr0.07540
X-RAY DIFFRACTIONf_plane_restr0.004585
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.0315-2.06180.2072880.1911573166153
2.0618-2.09410.2024820.18181751183360
2.0941-2.12840.23981050.18321901200665
2.1284-2.16510.2312950.18172086218170
2.1651-2.20450.21121130.18892175228874
2.2045-2.24680.22651240.19662325254979
2.2468-2.29270.25791310.19482487261885
2.2927-2.34250.24731450.19252572271788
2.3425-2.3970.22761410.17882678279191
2.397-2.4570.22331400.19532730287093
2.457-2.52340.24141420.1872825296796
2.5234-2.59760.23411480.20772856300497
2.5976-2.68140.25441700.19212840301098
2.6814-2.77720.27981570.20512895305299
2.7772-2.88840.27681420.18862951309399
2.8884-3.01980.22441770.194529123089100
3.0198-3.17890.21531600.189429053065100
3.1789-3.3780.25341430.184229563099100
3.378-3.63860.21111600.182629233065100
3.6386-4.00440.21441630.162229433106100
4.0044-4.5830.17161270.13829443071100
4.583-5.77060.14751630.149129433106100
5.7706-37.42210.1961450.19412820296596
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)
11.1513-0.94840.22291.3713-0.16220.82320.24670.2465-0.1584-0.1892-0.19910.03970.0185-0.02620.05720.20720.1224-0.03780.1889-0.0290.132973.412762.3588-21.1014
21.2349-0.30710.522.215-0.33671.1961-0.0061-0.0142-0.1330.02320.01820.3533-0.0643-0.24140.04790.14390.0615-0.00210.23160.02340.179556.162977.5172-24.5232
31.6443-1.37330.10061.5156-0.19821.1038-0.1152-0.0957-0.12240.08270.0911-0.01790.03630.01360.02080.09780.03230.03070.1140.00630.116272.854163.37922.6924
41.6767-0.46240.0591.7216-0.06561.42230.0251-0.03120.2060.04480.0047-0.1674-0.254-0.00490.00680.13790.02220.04090.090.00070.123861.863183.37965.6791
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 42:182 )
2X-RAY DIFFRACTION2(CHAIN A AND RESID 183:244 )
3X-RAY DIFFRACTION3(CHAIN B AND RESID 40:182 )
4X-RAY DIFFRACTION4(CHAIN B AND RESID 183:245 )

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