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- PDB-7gr7: Crystal Structure of PAS-GAF domain of the phytochrome from Deino... -

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Basic information

Entry
Database: PDB / ID: 7gr7
TitleCrystal Structure of PAS-GAF domain of the phytochrome from Deinococcus radiodurans at femto and picosecond timescales (295 fs)
ComponentsBacteriophytochrome
KeywordsTRANSFERASE / Phytochrome / Serial femtosecond crystallography / photoresponse
Function / homology
Function and homology information


osmosensory signaling via phosphorelay pathway / detection of visible light / phosphorelay response regulator activity / histidine kinase / phosphorelay sensor kinase activity / protein kinase activator activity / photoreceptor activity / regulation of DNA-templated transcription / ATP binding / identical protein 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. / Signal transduction histidine kinase-related protein, C-terminal / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily ...: / Phytochrome, PHY domain superfamily / PAS fold-2 / PAS fold / Phytochrome, central region / Phytochrome region / Phytochrome chromophore attachment domain / Phytochrome chromophore attachment site domain profile. / 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 / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / PAS domain superfamily / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase superfamily
Similarity search - Domain/homology
Chem-LBV / Bacteriophytochrome
Similarity search - Component
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 2.12 Å
AuthorsShankar, M.K. / Westenhoff, S.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)279944European Union
CitationJournal: To be published
Title: Crystal Structure of PAS-GAF domain of the phytochrome from Deinococcus radiodurans at femto and picosecond timescales
Authors: Shankar, M.K. / Westenhoff, S.
History
DepositionNov 7, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 1, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bacteriophytochrome
B: Bacteriophytochrome
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,6304
Polymers74,4592
Non-polymers1,1712
Water5,152286
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5430 Å2
ΔGint-37 kcal/mol
Surface area25860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.950, 116.500, 117.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Bacteriophytochrome / Phytochrome-like protein


Mass: 37229.453 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans (radioresistant)
Gene: bphP, DR_A0050 / Plasmid: pET21b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9RZA4, histidine kinase
#2: Chemical ChemComp-LBV / 3-[2-[(Z)-[3-(2-carboxyethyl)-5-[(Z)-(4-ethenyl-3-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-4-methyl-pyrrol-1-ium -2-ylidene]methyl]-5-[(Z)-[(3E)-3-ethylidene-4-methyl-5-oxidanylidene-pyrrolidin-2-ylidene]methyl]-4-methyl-1H-pyrrol-3- yl]propanoic acid / 2(R),3(E)- PHYTOCHROMOBILIN


Mass: 585.670 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C33H37N4O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 286 / 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: 2.45 Å3/Da / Density % sol: 49.9 %
Crystal growTemperature: 298 K / Method: batch mode / pH: 4.95
Details: 60 mM sodium acetate, 3.3% PEG400, 1 mM DTT, 30% MPD

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: FREE ELECTRON LASER / Site: SACLA / Beamline: BL3 / Wavelength: 1.7712 Å
DetectorType: MPCCD / Detector: CCD / Date: Jun 24, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.7712 Å / Relative weight: 1
ReflectionResolution: 2.12→33.07 Å / Num. obs: 41974 / % possible obs: 100 % / Redundancy: 118 % / CC1/2: 0.97 / CC star: 0.99 / Net I/σ(I): 8.07
Serial crystallography sample deliveryMethod: injection

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
CrystFELdata scaling
CrystFELdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.12→10 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 28.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.21 1907 4.7 %
Rwork0.2017 --
obs0.2021 40533 93.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.12→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4880 0 0 286 5166
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015085
X-RAY DIFFRACTIONf_angle_d1.3876974
X-RAY DIFFRACTIONf_dihedral_angle_d16.1111886
X-RAY DIFFRACTIONf_chiral_restr0.076790
X-RAY DIFFRACTIONf_plane_restr0.016915
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.12-2.170.44151260.45262142X-RAY DIFFRACTION75
2.17-2.230.4151280.4392470X-RAY DIFFRACTION85
2.23-2.30.36891330.39132611X-RAY DIFFRACTION89
2.3-2.370.39331440.39182649X-RAY DIFFRACTION92
2.37-2.450.41441360.3622690X-RAY DIFFRACTION93
2.45-2.550.33851090.33282807X-RAY DIFFRACTION95
2.55-2.660.31311430.31672776X-RAY DIFFRACTION96
2.66-2.80.28531510.31252819X-RAY DIFFRACTION97
2.8-2.970.29811260.27582882X-RAY DIFFRACTION98
2.97-3.190.2261330.22882895X-RAY DIFFRACTION98
3.19-3.50.19451660.18612895X-RAY DIFFRACTION98
3.5-3.980.14821460.13742927X-RAY DIFFRACTION99
3.98-4.910.08521430.08122986X-RAY DIFFRACTION99
4.92-100.07331230.07563077X-RAY DIFFRACTION98

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