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- PDB-4q0h: Deinococcus radiodurans BphP PAS-GAF -

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Basic information

Entry
Database: PDB / ID: 4q0h
TitleDeinococcus radiodurans BphP PAS-GAF
ComponentsBacteriophytochrome
KeywordsTRANSFERASE / PAS GAF / photosensor / response regulator
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 / phosphorelay sensor kinase 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. / GAF domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / PAS 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. / GAF domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / PAS domain / 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 / PAS domain superfamily / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ISOPROPYL ALCOHOL / Chem-LBV / Bacteriophytochrome
Similarity search - Component
Biological speciesDeinococcus radiodurans R1 (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.157 Å
AuthorsBurgie, E.S. / Vierstra, R.D.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Crystallographic and Electron Microscopic Analyses of a Bacterial Phytochrome Reveal Local and Global Rearrangements during Photoconversion.
Authors: Burgie, E.S. / Wang, T. / Bussell, A.N. / Walker, J.M. / Li, H. / Vierstra, R.D.
History
DepositionApr 2, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 16, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 17, 2014Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / struct_ref_seq_dif / struct_site
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bacteriophytochrome
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8266
Polymers37,0241
Non-polymers8015
Water6,990388
1
A: Bacteriophytochrome
hetero molecules

A: Bacteriophytochrome
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,65112
Polymers74,0492
Non-polymers1,60310
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area6720 Å2
ΔGint-44 kcal/mol
Surface area26040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.536, 51.608, 80.633
Angle α, β, γ (deg.)90.00, 116.32, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-535-

HOH

21A-632-

HOH

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Components

#1: Protein Bacteriophytochrome / Phytochrome-like protein


Mass: 37024.250 Da / Num. of mol.: 1 / Fragment: PAS-GAF / Mutation: Y307S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans R1 (radioresistant)
Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422
Gene: bphP, DR_A0050 / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9RZA4, histidine kinase
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / Isopropyl alcohol


Mass: 60.095 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#4: 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.: 1 / Source method: obtained synthetically / Formula: C33H37N4O6
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 388 / 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: 2.25 Å3/Da / Density % sol: 45.45 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 10% PEG 3350, 19% isopropanol, 5% glycerol, 100 mM citric acid(NaOH) ph 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.6888 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 30, 2013
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.6888 Å / Relative weight: 1
ReflectionResolution: 1.157→50 Å / Num. all: 113853 / Num. obs: 111918 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.157→36.137 Å / SU ML: 0.1 / σ(F): 1.34 / Phase error: 15.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1571 2010 1.8 %
Rwork0.1307 --
obs0.1312 111904 97.43 %
all-114856 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.157→36.137 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2429 0 56 388 2873
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093571
X-RAY DIFFRACTIONf_angle_d1.3284934
X-RAY DIFFRACTIONf_dihedral_angle_d16.1011377
X-RAY DIFFRACTIONf_chiral_restr0.075547
X-RAY DIFFRACTIONf_plane_restr0.009668
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1568-1.18570.24321260.23986688X-RAY DIFFRACTION84
1.1857-1.21780.24161520.21117755X-RAY DIFFRACTION97
1.2178-1.25360.19921300.19067858X-RAY DIFFRACTION98
1.2536-1.29410.18921420.17197879X-RAY DIFFRACTION98
1.2941-1.34030.16561450.15617782X-RAY DIFFRACTION98
1.3403-1.3940.18831490.14597909X-RAY DIFFRACTION98
1.394-1.45740.15341350.13247871X-RAY DIFFRACTION98
1.4574-1.53430.14181570.1167900X-RAY DIFFRACTION98
1.5343-1.63040.13161350.10797957X-RAY DIFFRACTION99
1.6304-1.75630.14091420.11367995X-RAY DIFFRACTION99
1.7563-1.9330.12341490.12327967X-RAY DIFFRACTION99
1.933-2.21270.16591540.11918032X-RAY DIFFRACTION99
2.2127-2.78760.1351450.12798081X-RAY DIFFRACTION99
2.7876-36.15430.16671490.13038220X-RAY DIFFRACTION100

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