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- PDB-8f71: Crystal structure of the histidine kinase domain of bacteriophyto... -

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Basic information

Entry
Database: PDB / ID: 8f71
TitleCrystal structure of the histidine kinase domain of bacteriophytochrome RpBphP2
ComponentsHistidine kinase
KeywordsSIGNALING PROTEIN / TRANSFERASE / Histidine kinase / Bacteriophytochrome
Function / homology
Function and homology information


detection of visible light / histidine kinase / photoreceptor activity / phosphorelay sensor kinase activity / regulation of DNA-templated transcription / ATP binding / metal ion binding
Similarity search - Function
Phytochrome, PHY domain superfamily / PAS fold-2 / PAS fold / Phytochrome, central region / Phytochrome region / Phytochrome chromophore attachment domain / Phytochrome chromophore attachment site domain profile. / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain ...Phytochrome, PHY domain superfamily / PAS fold-2 / PAS fold / Phytochrome, central region / Phytochrome region / Phytochrome chromophore attachment domain / Phytochrome chromophore attachment site domain profile. / 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 / Signal transduction histidine kinase-related protein, C-terminal / Histidine kinase domain / Histidine kinase domain profile. / GAF domain / Domain present in phytochromes and cGMP-specific phosphodiesterases. / GAF domain / GAF-like domain superfamily / 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
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / histidine kinase
Similarity search - Component
Biological speciesRhodopseudomonas palustris CGA009 (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.19 Å
AuthorsYang, X. / Kumarapperuma, I. / Tom, I.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Eye Institute (NIH/NEI)EY024363 United States
CitationJournal: Photochem Photobiol Sci / Year: 2023
Title: Mode of autophosphorylation in bacteriophytochromes RpBphP2 and RpBphP3.
Authors: Kumarapperuma, I. / Tom, I.P. / Bandara, S. / Montano, S. / Yang, X.
History
DepositionNov 17, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 22, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histidine kinase
B: Histidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,1856
Polymers59,1222
Non-polymers1,0634
Water724
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2470 Å2
ΔGint-24 kcal/mol
Surface area22950 Å2
Unit cell
Length a, b, c (Å)84.851, 84.851, 346.060
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6

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Components

#1: Protein Histidine kinase /


Mass: 29560.869 Da / Num. of mol.: 2 / Fragment: histidine kinase domain (UNP residues 506-758)
Source method: isolated from a genetically manipulated source
Details: ATP
Source: (gene. exp.) Rhodopseudomonas palustris CGA009 (phototrophic)
Gene: phyB1, RPA3015 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6N5G3, histidine kinase
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.99 Å3/Da / Density % sol: 58.91 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 25% PEG3350, 0.2 M sodium chloride, 0.1 M Tris-HCl, pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.9787 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 3.19→50 Å / Num. obs: 22330 / % possible obs: 99.5 % / Redundancy: 8.6 % / Biso Wilson estimate: 102.67 Å2 / Rpim(I) all: 0.041 / Net I/σ(I): 17.8
Reflection shellResolution: 3.2→3.26 Å / Redundancy: 8.8 % / Num. unique obs: 645 / Rpim(I) all: 0.429 / % possible all: 97.8

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
HKL-2000data scaling
AutoSolphasing
HKL-2000data reduction
RefinementMethod to determine structure: SAD / Resolution: 3.19→42.11 Å / SU ML: 0.49 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2643 1103 4.94 %
Rwork0.2218 --
obs0.2238 22330 96.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.19→42.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3090 0 64 4 3158
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005
X-RAY DIFFRACTIONf_angle_d0.924
X-RAY DIFFRACTIONf_dihedral_angle_d7.016440
X-RAY DIFFRACTIONf_chiral_restr0.057473
X-RAY DIFFRACTIONf_plane_restr0.009570
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.19-3.340.35531440.33132686X-RAY DIFFRACTION98
3.34-3.520.39291390.30792671X-RAY DIFFRACTION97
3.52-3.740.27511370.26322617X-RAY DIFFRACTION96
3.74-4.020.26621320.24092650X-RAY DIFFRACTION96
4.02-4.430.23991360.20882663X-RAY DIFFRACTION97
4.43-5.070.22781440.19562634X-RAY DIFFRACTION96
5.07-6.380.26941410.23322643X-RAY DIFFRACTION96
6.38-42.110.25241300.18692663X-RAY DIFFRACTION97
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)
13.68531.39652.63953.13432.12594.64240.1390.6557-0.50450.21520.4047-0.62810.57651.0292-0.57150.81820.1657-0.10410.9049-0.32190.895380.401722.6786155.1875
22.3696-1.8007-3.71231.57522.47877.0003-0.15150.1508-0.31090.3270.01810.36970.7208-0.20840.18660.8595-0.0262-0.00350.6722-0.18770.888541.267318.7615166.6531
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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