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- PDB-5k5b: Wild-type PAS-GAF fragment from Deinococcus radiodurans BphP -

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Basic information

Entry
Database: PDB / ID: 5k5b
TitleWild-type PAS-GAF fragment from Deinococcus radiodurans BphP
ComponentsBacteriophytochrome
KeywordsTRANSFERASE / Kinase Photosensor Transferase 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. / 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
ACETATE ION / Chem-LBV / Bacteriophytochrome
Similarity search - Component
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsTakala, H. / Edlund, P. / Claesson, E. / Ihalainen, J.A. / Westenhoff, S.
CitationJournal: Sci Rep / Year: 2016
Title: The room temperature crystal structure of a bacterial phytochrome determined by serial femtosecond crystallography.
Authors: Edlund, P. / Takala, H. / Claesson, E. / Henry, L. / Dods, R. / Lehtivuori, H. / Panman, M. / Pande, K. / White, T. / Nakane, T. / Berntsson, O. / Gustavsson, E. / Bath, P. / Modi, V. / Roy- ...Authors: Edlund, P. / Takala, H. / Claesson, E. / Henry, L. / Dods, R. / Lehtivuori, H. / Panman, M. / Pande, K. / White, T. / Nakane, T. / Berntsson, O. / Gustavsson, E. / Bath, P. / Modi, V. / Roy-Chowdhury, S. / Zook, J. / Berntsen, P. / Pandey, S. / Poudyal, I. / Tenboer, J. / Kupitz, C. / Barty, A. / Fromme, P. / Koralek, J.D. / Tanaka, T. / Spence, J. / Liang, M. / Hunter, M.S. / Boutet, S. / Nango, E. / Moffat, K. / Groenhof, G. / Ihalainen, J. / Stojkovic, E.A. / Schmidt, M. / Westenhoff, S.
History
DepositionMay 23, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 26, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 2, 2016Group: Database references
Revision 1.2Jan 10, 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

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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)38,1106
Polymers37,2291
Non-polymers8815
Water5,801322
1
A: Bacteriophytochrome
hetero molecules

A: Bacteriophytochrome
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,22112
Polymers74,4592
Non-polymers1,76210
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area5450 Å2
ΔGint-56 kcal/mol
Surface area27130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.760, 54.280, 70.150
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: 37229.453 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans (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-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#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
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 322 / 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: 2.4 Å3/Da / Density % sol: 48.66 %
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: ID23-1 / Wavelength: 0.972957 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 12, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972957 Å / Relative weight: 1
ReflectionResolution: 1.35→46.97 Å / Num. obs: 75872 / % possible obs: 98.1 % / Observed criterion σ(I): -3 / Redundancy: 4.36 % / Biso Wilson estimate: 25.092 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.036 / Net I/σ(I): 18.37
Reflection shell
Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.35-1.384.230.562.31195.7
1.38-20.1119.69197.8
2-2.40.03630.68199
2.4-30.02940.38199.6
3-40.02647.74199.3
4-80.02951.24199.4
8-150.03453.421100
150.03648.35189.7

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEOct 15, 2015data scaling
PHASER2.5.7phasing
REFMAC5.8.0135refinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Q0H

4q0h


Resolution: 1.35→39.37 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.97 / SU B: 1.483 / SU ML: 0.027 / SU R Cruickshank DPI: 0.0479 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.048 / ESU R Free: 0.047
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1709 3795 5 %RANDOM
Rwork0.1407 ---
obs0.1422 72086 98.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 78.41 Å2 / Biso mean: 25.474 Å2 / Biso min: 11.78 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20 Å2-0.2 Å2
2--0 Å20 Å2
3----0.07 Å2
Refinement stepCycle: final / Resolution: 1.35→39.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2335 0 63 322 2720
Biso mean--21.22 36.73 -
Num. residues----306
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0192576
X-RAY DIFFRACTIONr_angle_refined_deg1.5062.0063537
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3275326
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.03923.143105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.68415390
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.911520
X-RAY DIFFRACTIONr_chiral_restr0.0850.2401
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0221996
X-RAY DIFFRACTIONr_mcbond_it1.6752.2161279
X-RAY DIFFRACTIONr_mcangle_it2.2353.3111606
X-RAY DIFFRACTIONr_scbond_it2.1342.4811296
X-RAY DIFFRACTIONr_rigid_bond_restr1.65432575
X-RAY DIFFRACTIONr_sphericity_free30.668583
X-RAY DIFFRACTIONr_sphericity_bonded13.88852744
LS refinement shellResolution: 1.35→1.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 275 -
Rwork0.26 5211 -
all-5486 -
obs--95.69 %

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