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- PDB-3a0w: Catalytic domain of histidine kinase ThkA (TM1359) for MAD phasin... -

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Basic information

Entry
Database: PDB / ID: 3a0w
TitleCatalytic domain of histidine kinase ThkA (TM1359) for MAD phasing (nucleotide free form 2, orthorombic)
ComponentsSensor protein
KeywordsTRANSFERASE / ATP-lid / Kinase / Phosphoprotein / Two-component regulatory system
Function / homology
Function and homology information


histidine kinase / phosphorelay sensor kinase activity / 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 / Histidine kinase/HSP90-like ATPase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ETHYL MERCURY ION / 2-(ETHYLMERCURI-THIO)-BENZOIC ACID / histidine kinase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.69 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 24, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Sensor protein
B: Sensor protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9909
Polymers35,4522
Non-polymers1,5387
Water4,179232
1
A: Sensor protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6875
Polymers17,7261
Non-polymers9604
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Sensor protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3044
Polymers17,7261
Non-polymers5773
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.092, 61.148, 90.287
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: Chemical
ChemComp-EMC / ETHYL MERCURY ION


Mass: 229.651 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H5Hg
#3: Chemical ChemComp-EMT / 2-(ETHYLMERCURI-THIO)-BENZOIC ACID


Mass: 382.830 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H10HgO2S
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / 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: 2.3 Å3/Da / Density % sol: 46.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5
Details: 40% MPD, 0.1M sodium cacodylate, 5% PEG8000, pH 6.5, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1.0072, 1.0090, 0.9900
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: May 30, 2006
RadiationMonochromator: Si 111 DOUBLE CRYSTAL MONOCHROMATOR / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.00721
21.0091
30.991
ReflectionResolution: 1.69→20 Å / Num. obs: 36504 / % possible obs: 97.5 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Biso Wilson estimate: 21.8 Å2 / Rsym value: 0.069 / Net I/σ(I): 25.4
Reflection shellResolution: 1.69→1.75 Å / Redundancy: 3 % / Mean I/σ(I) obs: 4.7 / Rsym value: 0.305 / % possible all: 93

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT3.006data extraction
SPACEdata collection
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.69→20 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.934 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 2.286 / SU ML: 0.078 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.127 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24 1832 5 %RANDOM
Rwork0.213 ---
obs0.214 36456 97.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 99.86 Å2 / Biso mean: 23.063 Å2 / Biso min: 8.95 Å2
Baniso -1Baniso -2Baniso -3
1-0.4 Å20 Å20 Å2
2---0.87 Å20 Å2
3---0.47 Å2
Refinement stepCycle: LAST / Resolution: 1.69→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2499 0 47 232 2778
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222594
X-RAY DIFFRACTIONr_angle_refined_deg1.4741.9793483
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6985306
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.29324.697132
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.14615508
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.651520
X-RAY DIFFRACTIONr_chiral_restr0.1040.2386
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021920
X-RAY DIFFRACTIONr_nbd_refined0.2120.21236
X-RAY DIFFRACTIONr_nbtor_refined0.3130.21784
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.2213
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2230.263
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1670.216
X-RAY DIFFRACTIONr_mcbond_it1.1721.51567
X-RAY DIFFRACTIONr_mcangle_it1.84922479
X-RAY DIFFRACTIONr_scbond_it2.69831159
X-RAY DIFFRACTIONr_scangle_it4.0354.5997
LS refinement shellResolution: 1.688→1.732 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 103 -
Rwork0.294 2421 -
all-2524 -
obs--93.52 %

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