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- PDB-6oza: Crystal structure of the phycocyanobilin-bound GAF domain from a ... -

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Basic information

Entry
Database: PDB / ID: 6oza
TitleCrystal structure of the phycocyanobilin-bound GAF domain from a cyanobacterial phytochrome
ComponentsTwo-component sensor histidine kinase
KeywordsTRANSFERASE / cyanobacterial phytochromes / photoreceptors / SIGNALING PROTEIN
Function / homology
Function and homology information


detection of visible light / phosphorelay sensor kinase activity / photoreceptor activity / regulation of DNA-templated transcription
Similarity search - Function
Phytochrome, central region / Phytochrome region / Phytochrome chromophore attachment domain / Phytochrome chromophore attachment site domain profile. / GAF domain / 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 ...Phytochrome, central region / Phytochrome region / Phytochrome chromophore attachment domain / Phytochrome chromophore attachment site domain profile. / GAF domain / 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 / Beta-Lactamase / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PHYCOCYANOBILIN / Two-component sensor histidine kinase
Similarity search - Component
Biological speciesNostoc sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.002 Å
AuthorsHeewhan, S. / Xiaoli, Z. / Yafang, S. / Zhong, R. / Wolfgang, G. / Kai, H.Z. / Xiaojing, Y.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R01EY024363 United States
Other privateCBC C-086 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: The interplay between chromophore and protein determines the extended excited state dynamics in a single-domain phytochrome.
Authors: Slavov, C. / Fischer, T. / Barnoy, A. / Shin, H. / Rao, A.G. / Wiebeler, C. / Zeng, X. / Sun, Y. / Xu, Q. / Gutt, A. / Zhao, K.H. / Gartner, W. / Yang, X. / Schapiro, I. / Wachtveitl, J.
History
DepositionMay 15, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jul 8, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Jul 29, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Two-component sensor histidine kinase
B: Two-component sensor histidine kinase
C: Two-component sensor histidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,8536
Polymers69,0873
Non-polymers1,7663
Water99155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5890 Å2
ΔGint-87 kcal/mol
Surface area25790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.833, 78.833, 208.854
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Two-component sensor histidine kinase


Mass: 23029.117 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) (bacteria)
Gene: all2699 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8YTL8
#2: Chemical ChemComp-CYC / PHYCOCYANOBILIN / Phycocyanobilin


Mass: 588.694 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C33H40N4O6
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 55 / 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: 2.65 Å3/Da / Density % sol: 53.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: PEG 4000, ammonium acetate, sodium citrate tribasic dihydrate. Crystal was grown in dark.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.979 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Dec 25, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 15740 / % possible obs: 100 % / Redundancy: 10.6 % / Net I/σ(I): 3.1
Reflection shellResolution: 3→3.05 Å / Num. unique obs: 747

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.002→48.744 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.92
RfactorNum. reflection% reflection
Rfree0.2436 1561 9.95 %
Rwork0.1922 --
obs0.1973 15687 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.002→48.744 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4272 0 129 55 4456
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094517
X-RAY DIFFRACTIONf_angle_d1.1426151
X-RAY DIFFRACTIONf_dihedral_angle_d14.4841629
X-RAY DIFFRACTIONf_chiral_restr0.036710
X-RAY DIFFRACTIONf_plane_restr0.004791
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0024-3.09930.31511350.25991239X-RAY DIFFRACTION98
3.0993-3.210.33311430.26531256X-RAY DIFFRACTION100
3.21-3.33850.31381370.2441253X-RAY DIFFRACTION100
3.3385-3.49040.26841410.21461266X-RAY DIFFRACTION100
3.4904-3.67440.23471400.20681279X-RAY DIFFRACTION100
3.6744-3.90450.25881370.19391276X-RAY DIFFRACTION100
3.9045-4.20580.21671390.16931274X-RAY DIFFRACTION100
4.2058-4.62880.2231450.15481288X-RAY DIFFRACTION100
4.6288-5.29790.19491450.1531295X-RAY DIFFRACTION100
5.2979-6.67210.25831450.19731312X-RAY DIFFRACTION100
6.6721-48.75070.19541540.17011388X-RAY DIFFRACTION99
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)
13.699-1.2225-2.01280.70290.72143.3389-0.0034-0.0525-0.21050.0358-0.0850.00930.07110.00020.08250.2383-0.0064-0.02790.22320.01380.32582.37837.974518.7747
24.09721.38191.98481.26220.85923.0172-0.0977-0.06430.18080.0179-0.01060.1545-0.0355-0.11560.0960.24690.00870.0050.22620.04310.349840.661819.690719.6439
30.9347-0.66310.04345.4943-2.26732.9225-0.0566-0.129-0.0461-0.02260.0254-0.09890.0124-0.00480.04020.2576-0.00540.01290.27510.0020.352732.0847-18.8617.8206
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C

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