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- PDB-3a0z: Catalytic domain of histidine kinase ThkA (TM1359) (nucleotide fr... -

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Basic information

Entry
Database: PDB / ID: 3a0z
TitleCatalytic domain of histidine kinase ThkA (TM1359) (nucleotide free form 4: isopropanol, 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: 1.75 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
Water5,260292
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
MethodPISA
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
MethodPISA
Unit cell
Length a, b, c (Å)58.310, 61.094, 89.952
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.: 292 / 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: 2.26 Å3/Da / Density % sol: 45.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5.6
Details: 20% isopropanol, 0.1M sodium citrate, 20% PEG4000, pH 5.6, 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: Jun 1, 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: 1.75→50 Å / Num. obs: 31968 / % possible obs: 96 % / Observed criterion σ(I): -3 / Redundancy: 5 % / Biso Wilson estimate: 19.1 Å2 / Rsym value: 0.044 / Net I/σ(I): 29.5
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 2.7 / Rsym value: 0.245 / % possible all: 86.3

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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: 1.75→30.77 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.923 / Occupancy max: 1 / Occupancy min: 0 / SU B: 2.475 / SU ML: 0.082 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.135 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.241 1621 5.1 %RANDOM
Rwork0.195 ---
obs0.198 31940 95.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 57.32 Å2 / Biso mean: 20.355 Å2 / Biso min: 8.71 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20 Å2
2---0.59 Å20 Å2
3---0.56 Å2
Refinement stepCycle: LAST / Resolution: 1.75→30.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2538 0 0 292 2830
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222588
X-RAY DIFFRACTIONr_angle_refined_deg1.4171.9653509
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7835324
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.0425140
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.52515517
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5211520
X-RAY DIFFRACTIONr_chiral_restr0.0990.2389
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021968
X-RAY DIFFRACTIONr_nbd_refined0.2070.21214
X-RAY DIFFRACTIONr_nbtor_refined0.3120.21805
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.2238
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1530.243
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1720.211
X-RAY DIFFRACTIONr_mcbond_it0.991.51587
X-RAY DIFFRACTIONr_mcangle_it1.57422511
X-RAY DIFFRACTIONr_scbond_it2.41931134
X-RAY DIFFRACTIONr_scangle_it3.5454.5981
LS refinement shellResolution: 1.747→1.792 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 89 -
Rwork0.229 1921 -
all-2010 -
obs--83.13 %

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