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- PDB-8c3i: Dark state of PAS-GAF fragment from Deinococcus radiodurans phyto... -

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Basic information

Entry
Database: PDB / ID: 8c3i
TitleDark state of PAS-GAF fragment from Deinococcus radiodurans phytochrome
ComponentsBacteriophytochrome
KeywordsTRANSFERASE / Photoactive protein / bilin / Serial crystallography
Function / homology
Function and homology information


osmosensory signaling via phosphorelay pathway / detection of visible light / phosphorelay response regulator activity / protein kinase activator activity / histidine kinase / photoreceptor activity / phosphorelay sensor kinase 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, dimerisation/phosphoacceptor domain superfamily / Signal transduction histidine kinase-related protein, C-terminal / Histidine kinase 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. / 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 / Histidine kinase-like ATPases / PAS domain superfamily / Histidine kinase/HSP90-like ATPase / 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: 2.1 Å
AuthorsMadan Kumar, S. / Sebastian, W.
Funding supportEuropean Union, Japan, Finland, 3items
OrganizationGrant numberCountry
European Research Council (ERC)279944European Union
Japan Agency for Medical Research and Development (AMED) Japan
Academy of Finland285461 Finland
CitationJournal: To Be Published
Title: Dark state of PAS-GAF fragment from Deinococcus radiodurans phytochrome
Authors: Madan Kumar, S. / Sebastian, W.
History
DepositionDec 24, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 10, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Bacteriophytochrome
A: Bacteriophytochrome
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,6304
Polymers74,4592
Non-polymers1,1712
Water3,693205
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
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
Details: Bacterophytochrome
Source: (gene. exp.) Deinococcus radiodurans (radioresistant)
Gene: bphP, DR_A0050 / 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.: 205 / 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: 2.45 Å3/Da / Density % sol: 55.55 %
Crystal growTemperature: 298 K / Method: batch mode / pH: 4.95
Details: 60 mM Sodium Acetate, 3.3% PEG400, 1 mM DTT, 30% 2-methyl-2,4-pentanediol

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SACLA / Beamline: BL3 / Wavelength: 1.7712 Å
DetectorType: MPCCD / Detector: CCD / Date: Jun 24, 2021
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.7712 Å / Relative weight: 1
ReflectionResolution: 2.1→33.07 Å / Num. obs: 50086 / % possible obs: 100 % / Redundancy: 18 % / CC1/2: 0.98 / CC star: 0.99 / R split: 0.1 / Net I/σ(I): 10
Reflection shellResolution: 2.1→10.3 Å / Num. unique obs: 1821 / CC1/2: 0.61 / CC star: 0.87 / % possible all: 100
Serial crystallography sample deliveryMethod: injection
Serial crystallography sample delivery injectionDescription: grease jet

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6T3L

6t3l


Resolution: 2.1→33.07 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.5 / Phase error: 17.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1962 2191 5.02 %
Rwork0.1609 --
obs0.1626 43639 97.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→33.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4794 0 86 205 5085
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085122
X-RAY DIFFRACTIONf_angle_d1.0847038
X-RAY DIFFRACTIONf_dihedral_angle_d16.0061877
X-RAY DIFFRACTIONf_chiral_restr0.064795
X-RAY DIFFRACTIONf_plane_restr0.009927
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.150.27011390.25192322X-RAY DIFFRACTION89
2.15-2.20.26241360.20152408X-RAY DIFFRACTION92
2.2-2.250.23421040.18342492X-RAY DIFFRACTION95
2.25-2.310.20151310.18372557X-RAY DIFFRACTION96
2.31-2.380.2671410.19262552X-RAY DIFFRACTION97
2.38-2.460.24091150.18672554X-RAY DIFFRACTION97
2.46-2.540.20531370.18272585X-RAY DIFFRACTION98
2.54-2.650.21791200.17152610X-RAY DIFFRACTION98
2.65-2.770.22841610.17552594X-RAY DIFFRACTION99
2.77-2.910.22391490.18622603X-RAY DIFFRACTION99
2.91-3.090.22811610.17012597X-RAY DIFFRACTION99
3.09-3.330.21521610.16432635X-RAY DIFFRACTION99
3.33-3.670.16041410.15072668X-RAY DIFFRACTION99
3.67-4.20.15811440.13262672X-RAY DIFFRACTION99
4.2-5.280.15131200.13112736X-RAY DIFFRACTION100
5.29-33.070.18361310.15962863X-RAY DIFFRACTION99

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