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- PDB-5nfx: Deinococcus radiodurans BphP PAS-GAF Y263F mutant -

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Basic information

Entry
Database: PDB / ID: 5nfx
TitleDeinococcus radiodurans BphP PAS-GAF Y263F 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 / GAF domain / Phytochrome chromophore attachment domain / Phytochrome chromophore attachment site domain profile. / PAS domain ...: / Phytochrome, PHY domain superfamily / PAS fold-2 / PAS fold / Phytochrome, central region / Phytochrome region / GAF domain / Phytochrome chromophore attachment domain / Phytochrome chromophore attachment site domain profile. / PAS domain / 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 / Beta-Lactamase / 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 / 2-Layer Sandwich / Alpha Beta
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: 1.34 Å
AuthorsTakala, H. / Westenhoff, S. / Ihalainen, J.A.
CitationJournal: J. Biol. Chem. / Year: 2018
Title: On the (un)coupling of the chromophore, tongue interactions, and overall conformation in a bacterial phytochrome.
Authors: Takala, H. / Lehtivuori, H.K. / Berntsson, O. / Hughes, A. / Nanekar, R. / Niebling, S. / Panman, M. / Henry, L. / Menzel, A. / Westenhoff, S. / Ihalainen, J.A.
History
DepositionMar 16, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 18, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 6, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.2Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model
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
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)38,0946
Polymers37,2131
Non-polymers8815
Water5,729318
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Crystallizes as monomer but dimer in solution.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2100 Å2
ΔGint-20 kcal/mol
Surface area14360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.240, 54.580, 70.560
Angle α, β, γ (deg.)90.000, 92.200, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Bacteriophytochrome / Phytochrome-like protein


Mass: 37213.453 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans R1 (radioresistant)
Gene: bphP, DR_A0050 / Plasmid: PET21B / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9RZA4, histidine kinase
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-MPD / (4S)-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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 318 / Source method: isolated from a natural source / Formula: H2O
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: 2.44 Å3/Da / Density % sol: 49.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.95
Details: sodium acetate, PEG 400, DTT, 2-methyl-2,4-pentanediol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 9, 2015
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 1.34→19.93 Å / Num. obs: 80229 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 4.127 % / Biso Wilson estimate: 24.857 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.059 / Rrim(I) all: 0.068 / Χ2: 0.94 / Net I/σ(I): 10.51 / Num. measured all: 331083 / Scaling rejects: 19
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.34-1.383.9431.3330.8959700.3111.53899.7
1.38-1.54.1970.8461.57169880.5660.96899.8
1.5-1.94.0580.2295.38289470.9650.26499.8
1.9-2.44.2580.0716.77142050.9940.0899.9
2.4-34.1350.04624.9168570.9960.05399.8
3-43.9240.03731.4541700.9970.04399.6
4-84.440.03537.2627180.9980.0499.7
8-154.0710.03737.553360.9980.04299.1
15-19.933.2890.03333.75380.9990.0455.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.33 Å19.93 Å
Translation1.33 Å19.93 Å

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALENov 1, 2016data scaling
PHASER2.5.6phasing
REFMAC5.8.0135refinement
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2O9C

2o9c


Resolution: 1.34→19.93 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.972 / SU B: 2.126 / SU ML: 0.036 / SU R Cruickshank DPI: 0.046 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.046 / ESU R Free: 0.048
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1823 4013 5 %RANDOM
Rwork0.1432 ---
obs0.1451 76244 99.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 106.05 Å2 / Biso mean: 25.452 Å2 / Biso min: 10.58 Å2
Baniso -1Baniso -2Baniso -3
1-0.39 Å2-0 Å2-1.23 Å2
2--0.14 Å2-0 Å2
3----0.44 Å2
Refinement stepCycle: final / Resolution: 1.34→19.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2336 0 63 318 2717
Biso mean--22.25 37.6 -
Num. residues----307
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0192577
X-RAY DIFFRACTIONr_bond_other_d0.0020.022484
X-RAY DIFFRACTIONr_angle_refined_deg1.7542.0063539
X-RAY DIFFRACTIONr_angle_other_deg0.99335700
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.655326
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.14523.333105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.05915388
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.241519
X-RAY DIFFRACTIONr_chiral_restr0.0990.2401
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212946
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02573
X-RAY DIFFRACTIONr_rigid_bond_restr2.55935059
X-RAY DIFFRACTIONr_sphericity_free40.65587
X-RAY DIFFRACTIONr_sphericity_bonded13.29855219
LS refinement shellResolution: 1.34→1.375 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.53 295 -
Rwork0.528 5617 -
all-5912 -
obs--99.73 %

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