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- PDB-3a0y: Catalytic domain of histidine kinase ThkA (TM1359) (nucleotide fr... -

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Basic information

Entry
Database: PDB / ID: 3a0y
TitleCatalytic domain of histidine kinase ThkA (TM1359) (nucleotide free form 3: 1,2-propanediol, orthorombic)
ComponentsSensor protein
KeywordsTRANSFERASE / ATP-lid / Kinase / Phosphoprotein / Two-component regulatory system
Function / homology
Function and homology information


phosphorelay sensor kinase activity / histidine kinase / regulation of DNA-templated transcription / ATP binding / metal ion binding
Similarity search - Function
His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / Signal transduction histidine kinase-related protein, C-terminal / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Histidine kinase domain / Histidine kinase domain profile. / Histidine kinase-like ATPase, C-terminal domain / Heat Shock Protein 90 / Domain present in phytochromes and cGMP-specific phosphodiesterases. ...His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / Signal transduction histidine kinase-related protein, C-terminal / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Histidine kinase domain / Histidine kinase domain profile. / Histidine kinase-like ATPase, C-terminal domain / Heat Shock Protein 90 / Domain present in phytochromes and cGMP-specific phosphodiesterases. / GAF domain / GAF-like domain superfamily / PAS fold / PAS fold / PAS domain / PAS repeat profile. / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / PAS domain / PAS domain superfamily / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 Å
AuthorsYamada, S. / Sugimoto, H. / Kobayashi, M. / Ohno, A. / Nakamura, H. / Shiro, Y.
CitationJournal: Structure / Year: 2009
Title: Structure of PAS-linked histidine kinase and the response regulator complex
Authors: Yamada, S. / Sugimoto, H. / Kobayashi, M. / Ohno, A. / Nakamura, H. / Shiro, Y.
History
DepositionMar 25, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sensor protein
B: Sensor protein


Theoretical massNumber of molelcules
Total (without water)35,4522
Polymers35,4522
Non-polymers00
Water3,027168
1
A: Sensor protein


Theoretical massNumber of molelcules
Total (without water)17,7261
Polymers17,7261
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Sensor protein


Theoretical massNumber of molelcules
Total (without water)17,7261
Polymers17,7261
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.688, 58.536, 87.085
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Sensor protein / Histidine kinase ThkA


Mass: 17726.236 Da / Num. of mol.: 2 / Fragment: catalytic domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM_1359 / Plasmid: pRSETA / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) CodonPlus RIL / References: UniProt: Q9X180, histidine kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 168 / 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: 2.15 Å3/Da / Density % sol: 42.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 4.5
Details: 25% 1,2-propanediol, 10% glycerol, 5% phosphate-citrate, 5% PEG3000, pH 4.5, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 3, 2007
RadiationMonochromator: Si 111 DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.57→20 Å / Num. obs: 41793 / % possible obs: 97.3 % / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Biso Wilson estimate: 18.9 Å2 / Rsym value: 0.04 / Net I/σ(I): 41.7
Reflection shellResolution: 1.57→1.64 Å / Redundancy: 5.4 % / Mean I/σ(I) obs: 3.3 / Rsym value: 0.444 / % possible all: 96.7

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT3.006data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3A0W

3a0w


Resolution: 1.57→19.61 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.941 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 1.596 / SU ML: 0.059 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.1 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.223 2074 5 %RANDOM
Rwork0.201 ---
obs0.202 41726 96.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 54.71 Å2 / Biso mean: 20.002 Å2 / Biso min: 9.72 Å2
Baniso -1Baniso -2Baniso -3
1-0.61 Å20 Å20 Å2
2---0.81 Å20 Å2
3---0.2 Å2
Refinement stepCycle: LAST / Resolution: 1.57→19.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2570 0 0 168 2738
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222635
X-RAY DIFFRACTIONr_angle_refined_deg1.3071.9643578
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4575330
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.70224.964139
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.7915525
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3771519
X-RAY DIFFRACTIONr_chiral_restr0.0970.2399
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021998
X-RAY DIFFRACTIONr_nbd_refined0.2080.21153
X-RAY DIFFRACTIONr_nbtor_refined0.3140.21850
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1280.2151
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.230.274
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1790.223
X-RAY DIFFRACTIONr_mcbond_it0.8511.51596
X-RAY DIFFRACTIONr_mcangle_it1.43422564
X-RAY DIFFRACTIONr_scbond_it2.26931154
X-RAY DIFFRACTIONr_scangle_it3.7314.5996
LS refinement shellResolution: 1.572→1.613 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.246 132 -
Rwork0.238 2625 -
all-2757 -
obs--88.76 %

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