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- PDB-7z9d: Deinococcus radiodurans BphP PAS-GAF H260A mutant -

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Basic information

Entry
Database: PDB / ID: 7z9d
TitleDeinococcus radiodurans BphP PAS-GAF H260A mutant
ComponentsBacteriophytochrome
KeywordsTRANSFERASE / KINASE / PHOTOSENSOR / PHYTOCHROME
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. / 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 / PAS domain superfamily / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily
Similarity search - Domain/homology
ACETATE ION / Chem-LBV / Bacteriophytochrome
Similarity search - Component
Biological speciesDeinococcus radiodurans R1 (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.88 Å
AuthorsTakala, H.
Funding support Finland, 1items
OrganizationGrant numberCountry
Academy of Finland285461, 330678 Finland
CitationJournal: Photochem Photobiol Sci / Year: 2022
Title: Conserved histidine and tyrosine determine spectral responses through the water network in Deinococcus radiodurans phytochrome.
Authors: Lehtivuori, H. / Rumfeldt, J. / Mustalahti, S. / Kurkinen, S. / Takala, H.
History
DepositionMar 21, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 10, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2022Group: 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
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)38,0436
Polymers37,1621
Non-polymers8815
Water4,774265
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Dimer in solution
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2110 Å2
ΔGint-21 kcal/mol
Surface area14560 Å2
Unit cell
Length a, b, c (Å)93.930, 54.390, 70.470
Angle α, β, γ (deg.)90.000, 92.390, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Bacteriophytochrome / Phytochrome-like protein


Mass: 37162.387 Da / Num. of mol.: 1 / Mutation: H260A
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 BL21(DE3) (bacteria) / References: UniProt: Q9RZA4, histidine kinase
#2: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*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 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 265 / 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: 2.42 Å3/Da / Density % sol: 49.17 %
Crystal growTemperature: 282 K / Method: vapor diffusion, hanging drop / pH: 4.95
Details: sodium acetate, PEG 400, DTT, 2-methyl-2,4-pentanediol
Temp details: cold room

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Dec 16, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.88→19.91 Å / Num. obs: 28767 / % possible obs: 98.9 % / Redundancy: 4.871 % / Biso Wilson estimate: 34.482 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.145 / Rrim(I) all: 0.163 / Χ2: 0.813 / Net I/σ(I): 7.38 / Num. measured all: 140132 / Scaling rejects: 15
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.88-1.934.6371.6830.679385208420240.3241.89797.1
1.93-24.9411.3970.9113804279527940.4121.563100
2-2.25.0110.831.7429795596059460.6870.92799.8
2.2-2.54.9550.4483.2528431575557380.8870.50299.7
2.5-34.8310.2086.625008522151770.970.23499.2
3-44.5790.0815.3718376414340130.9950.0996.9
4-65.0650.0525.8210980217421680.9980.05699.7
6-104.8920.04428.5335477287250.9980.0599.6
10-19.914.4290.02737.158062131820.9990.03185.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.88 Å19.91 Å
Translation1.88 Å19.91 Å

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASER2.5.7phasing
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSJun 1, 2017data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2O9C

2o9c


Resolution: 1.88→19.91 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.951 / SU B: 5.622 / SU ML: 0.146 / SU R Cruickshank DPI: 0.1481 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.148 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.225 1439 5 %RANDOM
Rwork0.1873 ---
obs0.1892 27327 98.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 122.82 Å2 / Biso mean: 36.495 Å2 / Biso min: 21.42 Å2
Baniso -1Baniso -2Baniso -3
1-0.34 Å2-0 Å2-1.48 Å2
2--0.17 Å20 Å2
3----0.38 Å2
Refinement stepCycle: final / Resolution: 1.88→19.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2352 0 63 265 2680
Biso mean--36.06 44.89 -
Num. residues----309
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0132567
X-RAY DIFFRACTIONr_bond_other_d0.0030.0152461
X-RAY DIFFRACTIONr_angle_refined_deg1.3431.6753524
X-RAY DIFFRACTIONr_angle_other_deg1.2111.5785653
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.045324
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.48821.157121
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.81615384
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.1561519
X-RAY DIFFRACTIONr_chiral_restr0.060.2329
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022926
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02562
LS refinement shellResolution: 1.88→1.928 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.416 102 -
Rwork0.423 1936 -
all-2038 -
obs--97.19 %

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