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- PDB-2vlg: KinA PAS-A domain, homodimer -

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Basic information

Entry
Database: PDB / ID: 2vlg
TitleKinA PAS-A domain, homodimer
ComponentsSPORULATION KINASE A
KeywordsTRANSFERASE / HISTIDINE KINASE / TWO-COMPONENT REGULATORY SYSTEM / TWO-COMPONENT SIGNAL TRANSDUCTION / SPORULATION / PHOSPHORYLATION / SCOD / SCOB / GSIC / SPOIIJ / KINASE / SPOIIF / PAS DOMAIN
Function / homology
Function and homology information


sporulation resulting in formation of a cellular spore / histidine kinase / phosphorelay sensor kinase activity / regulation of DNA-templated transcription / ATP binding / identical protein binding
Similarity search - Function
PAS fold-3 / PAS fold / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural 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 ...PAS fold-3 / PAS fold / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural 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 / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / PAS domain superfamily / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Sporulation kinase A
Similarity search - Component
Biological speciesBACILLUS SUBTILIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsLee, J. / Tomchick, D.R. / Brautigam, C.A. / Machius, M. / Kort, R. / Hellingwerf, K.J. / Gardner, K.H.
CitationJournal: Biochemistry / Year: 2008
Title: Changes at the Kina Pas-A Dimerization Interface Influence Histidine Kinase Function.
Authors: Lee, J. / Tomchick, D.R. / Brautigam, C.A. / Machius, M. / Kort, R. / Hellingwerf, K.J. / Gardner, K.H.
History
DepositionJan 14, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 18, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.4May 15, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SPORULATION KINASE A
B: SPORULATION KINASE A
C: SPORULATION KINASE A
D: SPORULATION KINASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,27210
Polymers52,0124
Non-polymers2606
Water5,423301
1
A: SPORULATION KINASE A
D: SPORULATION KINASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0413
Polymers26,0062
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area680 Å2
ΔGint-10 kcal/mol
Surface area13570 Å2
MethodPISA
2
B: SPORULATION KINASE A
C: SPORULATION KINASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2307
Polymers26,0062
Non-polymers2245
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area440 Å2
ΔGint-10 kcal/mol
Surface area13220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.568, 55.516, 78.879
Angle α, β, γ (deg.)90.00, 109.01, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
SPORULATION KINASE A / STAGE II SPORULATION PROTEIN J / KINA PAS-A


Mass: 13002.932 Da / Num. of mol.: 4 / Fragment: PAS-A, RESIDUES 10-117
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS SUBTILIS (bacteria) / Strain: STRAIN 1A40
Description: BACILLUS GENETIC STOCK CENTER, COLUMBUS, OH, U.S.A.
Plasmid: PHIS6GBETA1KINA / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P16497, histidine kinase
#2: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 301 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUES 7-9 (GEF) BELONG TO THE CLONING LINKER

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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: 2.1 Å3/Da / Density % sol: 42.4 % / Description: NONE
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 20 DEGREES CELSIUS, HANGING-DROP VAPOR DIFFUSION: 1 MICROLITER KINA (7 MG/ML IN 25 MM TRIS, PH 8, 100 MM NACL PLUS 1 MICROLITER WELL SOLUTION (13 TO 15% (W/V) PEG 10,000, 0.1 M AMMONIUM ...Details: 20 DEGREES CELSIUS, HANGING-DROP VAPOR DIFFUSION: 1 MICROLITER KINA (7 MG/ML IN 25 MM TRIS, PH 8, 100 MM NACL PLUS 1 MICROLITER WELL SOLUTION (13 TO 15% (W/V) PEG 10,000, 0.1 M AMMONIUM ACETATE, 0.1 M BIS-TRIS, PH 5.5); CRYSTALS APPEARED AFTER ABOUT ONE DAY AND GREW TO A FINAL SIZE OF ABOUT 80 X 80 X 100 MICROMETERS WITHIN FOUR DAYS; CRYO-PROTECTION: STEPWISE TRANSFER INTO WELL SOLUTION SUPPLEMENTED WITH UP TO 25% (V/V) GLYCEROL.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97924
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 12, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97924 Å / Relative weight: 1
ReflectionResolution: 1.71→44.75 Å / Num. obs: 42220 / % possible obs: 88 % / Observed criterion σ(I): -3 / Redundancy: 2.9 % / Biso Wilson estimate: 24.8 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 24.9
Reflection shellResolution: 1.71→1.74 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 1.9 / % possible all: 56

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Processing

Software
NameVersionClassification
REFMAC5.3.0037refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXphasing
MLPHAREphasing
DMphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.7→44 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.947 / SU B: 5.938 / SU ML: 0.097 / Cross valid method: THROUGHOUT / ESU R: 0.13 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.243 1499 3.5 %RANDOM
Rwork0.198 ---
obs0.2 40811 87.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.2 Å2
Baniso -1Baniso -2Baniso -3
1--1.51 Å20 Å2-0.07 Å2
2--2.99 Å20 Å2
3----1.53 Å2
Refinement stepCycle: LAST / Resolution: 1.7→44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3207 0 12 301 3520
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0223320
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7611.9414478
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7195390
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.56823.631157
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.79515613
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.491516
X-RAY DIFFRACTIONr_chiral_restr0.1240.2509
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022440
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2190.21388
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3190.22313
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.2297
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2010.284
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1970.220
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2221.52030
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.83423175
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.52731471
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.7324.51303
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.75 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.319 77
Rwork0.266 1758
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)
12.12220.0009-0.14511.0453-0.24023.7557-0.01670.12770.0201-0.04710.0003-0.0035-0.01440.12070.0163-0.03510.00460.0085-0.082-0.0289-0.047434.28039.49713.2805
23.31920.0509-0.82940.79360.37793.3929-0.0359-0.21930.06740.0230.0341-0.008-0.1050.41030.0019-0.0422-0.03770.0019-0.02750.0015-0.074844.68589.7815-9.8791
33.7766-0.32180.98010.85630.08932.06940.1309-0.3748-0.07920.0578-0.08350.08180.0243-0.1008-0.0474-0.0595-0.05860.0061-0.0144-0.0028-0.046922.44425.4054-24.1438
42.95960.1921-0.14941.34930.38712.75140.02420.18820.0061-0.0799-0.0447-0.03280.04-0.00410.0206-0.05960.0216-0.0075-0.03360.01-0.057429.04934.9231-47.2683
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A15 - 114
2X-RAY DIFFRACTION2B15 - 114
3X-RAY DIFFRACTION3C15 - 116
4X-RAY DIFFRACTION4D15 - 117

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