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- PDB-8k9o: Crystal structure of Cyanobacteriochrome RcaE GAF domain in Pg state -

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Basic information

Entry
Database: PDB / ID: 8k9o
TitleCrystal structure of Cyanobacteriochrome RcaE GAF domain in Pg state
Componentshistidine kinase
KeywordsSIGNALING PROTEIN / Cyanobacteriochrome / chromatic acclimation
Function / homology
Function and homology information


histidine kinase / phosphorelay sensor kinase activity
Similarity search - Function
: / PAS fold-4 / PAS fold / Phytochrome chromophore attachment domain / Phytochrome chromophore attachment site domain profile. / PAS domain / PAS-associated, C-terminal / PAC domain profile. / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain ...: / PAS fold-4 / PAS fold / Phytochrome chromophore attachment domain / Phytochrome chromophore attachment site domain profile. / PAS domain / PAS-associated, C-terminal / PAC domain profile. / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / Signal transduction histidine kinase-related protein, C-terminal / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Histidine kinase domain / Histidine kinase domain profile. / GAF domain / Domain present in phytochromes and cGMP-specific phosphodiesterases. / GAF domain / GAF-like domain superfamily / PAS domain / PAS repeat profile. / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / PAS domain / Histidine kinase-like ATPases / PAS domain superfamily / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily
Similarity search - Domain/homology
PHYCOCYANOBILIN / histidine kinase
Similarity search - Component
Biological speciesMicrochaete diplosiphon (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsNagae, T. / Hirose, Y. / Mishima, M.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)22H02562 Japan
Japan Society for the Promotion of Science (JSPS)19K06707 Japan
Other private Japan
CitationJournal: Sci Adv / Year: 2024
Title: Green/red light-sensing mechanism in the chromatic acclimation photosensor.
Authors: Nagae, T. / Fujita, Y. / Tsuchida, T. / Kamo, T. / Seto, R. / Hamada, M. / Aoyama, H. / Sato-Tomita, A. / Fujisawa, T. / Eki, T. / Miyanoiri, Y. / Ito, Y. / Soeta, T. / Ukaji, Y. / Unno, M. ...Authors: Nagae, T. / Fujita, Y. / Tsuchida, T. / Kamo, T. / Seto, R. / Hamada, M. / Aoyama, H. / Sato-Tomita, A. / Fujisawa, T. / Eki, T. / Miyanoiri, Y. / Ito, Y. / Soeta, T. / Ukaji, Y. / Unno, M. / Mishima, M. / Hirose, Y.
History
DepositionAug 1, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 15, 2024Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: histidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6342
Polymers22,0451
Non-polymers5891
Water1,31573
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1210 Å2
ΔGint-18 kcal/mol
Surface area10890 Å2
Unit cell
Length a, b, c (Å)64.273, 64.273, 84.116
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-571-

HOH

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Components

#1: Protein histidine kinase


Mass: 22045.102 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Microchaete diplosiphon (bacteria) / Gene: rcaE / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q47897, histidine kinase
#2: Chemical ChemComp-CYC / PHYCOCYANOBILIN


Mass: 588.694 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H40N4O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 1.97 Å3/Da / Density % sol: 37.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: PEG 8000, magnesium acetate, sodium cacodylate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: AichiSR / Beamline: BL2S1 / Wavelength: 1.1211 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 23, 2022
RadiationMonochromator: Ge(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1211 Å / Relative weight: 1
ReflectionResolution: 1.75→45.489 Å / Num. obs: 18446 / % possible obs: 100 % / Redundancy: 13.9 % / Biso Wilson estimate: 19.6 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.069 / Χ2: 0.98 / Net I/σ(I): 26.2
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 14.1 % / Rmerge(I) obs: 0.903 / Mean I/σ(I) obs: 3.4 / Num. unique obs: 1002 / CC1/2: 0.876 / Χ2: 1.01 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7CKV

7ckv


Resolution: 1.75→45.489 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.933 / SU B: 2.477 / SU ML: 0.08 / Cross valid method: FREE R-VALUE / ESU R: 0.124 / ESU R Free: 0.123
RfactorNum. reflection% reflection
Rfree0.2311 861 4.681 %
Rwork0.1875 17534 -
all0.19 --
obs-18395 99.962 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 24.374 Å2
Baniso -1Baniso -2Baniso -3
1-0.274 Å2-0 Å2-0 Å2
2--0.274 Å2-0 Å2
3----0.547 Å2
Refinement stepCycle: LAST / Resolution: 1.75→45.489 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1438 0 43 73 1554
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0131525
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161476
X-RAY DIFFRACTIONr_angle_refined_deg1.7061.6362080
X-RAY DIFFRACTIONr_angle_other_deg1.4491.5753386
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0945181
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.2823.03489
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.37315267
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.631158
X-RAY DIFFRACTIONr_chiral_restr0.090.2198
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021750
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02340
X-RAY DIFFRACTIONr_nbd_refined0.2110.2295
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1830.21410
X-RAY DIFFRACTIONr_nbtor_refined0.1660.2713
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.2718
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.261
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2210.223
X-RAY DIFFRACTIONr_nbd_other0.1790.290
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1220.213
X-RAY DIFFRACTIONr_mcbond_it2.1952.32718
X-RAY DIFFRACTIONr_mcbond_other2.1872.317717
X-RAY DIFFRACTIONr_mcangle_it2.9483.46895
X-RAY DIFFRACTIONr_mcangle_other2.9483.463896
X-RAY DIFFRACTIONr_scbond_it3.2852.697807
X-RAY DIFFRACTIONr_scbond_other3.2852.697806
X-RAY DIFFRACTIONr_scangle_it5.0273.9141183
X-RAY DIFFRACTIONr_scangle_other5.0253.9141184
X-RAY DIFFRACTIONr_lrange_it6.2628.031645
X-RAY DIFFRACTIONr_lrange_other6.2427.8951637
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.7950.307570.2261279X-RAY DIFFRACTION100
1.795-1.8450.296560.2231232X-RAY DIFFRACTION100
1.845-1.8980.312580.211211X-RAY DIFFRACTION100
1.898-1.9560.285660.2021161X-RAY DIFFRACTION100
1.956-2.020.25460.1831140X-RAY DIFFRACTION100
2.02-2.0910.224550.181088X-RAY DIFFRACTION100
2.091-2.170.233550.1731077X-RAY DIFFRACTION100
2.17-2.2580.235450.1651024X-RAY DIFFRACTION100
2.258-2.3590.19490.163987X-RAY DIFFRACTION100
2.359-2.4730.173470.163965X-RAY DIFFRACTION100
2.473-2.6070.199470.183875X-RAY DIFFRACTION100
2.607-2.7650.291530.183857X-RAY DIFFRACTION100
2.765-2.9550.226410.184812X-RAY DIFFRACTION100
2.955-3.1910.259410.196754X-RAY DIFFRACTION100
3.191-3.4940.213350.197704X-RAY DIFFRACTION100
3.494-3.9040.184300.179639X-RAY DIFFRACTION100
3.904-4.5040.217340.175574X-RAY DIFFRACTION100
4.504-5.5050.249270.178495X-RAY DIFFRACTION100
5.505-7.7410.234120.234407X-RAY DIFFRACTION99.5249
7.741-45.4890.30470.228253X-RAY DIFFRACTION98.1132

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