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- PDB-6t3u: PAS-GAF fragment from Deinococcus radiodurans phytochrome 1ps aft... -

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Basic information

Entry
Database: PDB / ID: 6t3u
TitlePAS-GAF fragment from Deinococcus radiodurans phytochrome 1ps after photoexcitation
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. / 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
Chem-LBV / Bacteriophytochrome
Similarity search - Component
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 2.21 Å
AuthorsClaesson, E. / Takala, H. / Yuan Wahlgren, W. / Pandey, S. / Schmidt, M. / Westenhoff, S.
Funding support Sweden, Japan, Finland, 4items
OrganizationGrant numberCountry
European Research Council279944 Sweden
Japan Agency for Medical Research and Development (AMED) Japan
Academy of Finland285461 Finland
Academy of Finland296135 Finland
CitationJournal: Elife / Year: 2020
Title: The primary structural photoresponse of phytochrome proteins captured by a femtosecond X-ray laser.
Authors: Claesson, E. / Wahlgren, W.Y. / Takala, H. / Pandey, S. / Castillon, L. / Kuznetsova, V. / Henry, L. / Panman, M. / Carrillo, M. / Kubel, J. / Nanekar, R. / Isaksson, L. / Nimmrich, A. / ...Authors: Claesson, E. / Wahlgren, W.Y. / Takala, H. / Pandey, S. / Castillon, L. / Kuznetsova, V. / Henry, L. / Panman, M. / Carrillo, M. / Kubel, J. / Nanekar, R. / Isaksson, L. / Nimmrich, A. / Cellini, A. / Morozov, D. / Maj, M. / Kurttila, M. / Bosman, R. / Nango, E. / Tanaka, R. / Tanaka, T. / Fangjia, L. / Iwata, S. / Owada, S. / Moffat, K. / Groenhof, G. / A Stojkovic, E. / A Ihalainen, J. / Schmidt, M. / Westenhoff, S.
History
DepositionOct 11, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 8, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2023Group: 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 / pdbx_related_exp_data_set
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 1.2Jan 24, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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
Water2,648147
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5580 Å2
ΔGint-35 kcal/mol
Surface area26470 Å2
Unit cell
Length a, b, c (Å)54.980, 116.690, 117.860
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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
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 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 / Water


Mass: 18.015 Da / Num. of mol.: 147 / 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: 49.82 %
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: Oct 12, 2018
RadiationMonochromator: graphite crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.7712 Å / Relative weight: 1
ReflectionResolution: 2.21→41.46 Å / Num. obs: 39316 / % possible obs: 100 % / Redundancy: 106.11 % / CC1/2: 0.98 / R split: 0.1059 / Net I/σ(I): 6.1
Reflection shellResolution: 2.21→2.25 Å / Redundancy: 34.3 % / Mean I/σ(I) obs: 0.88 / Num. unique obs: 1512 / CC1/2: 0.38 / R split: 1.1464 / % possible all: 100
Serial crystallography sample deliveryDescription: grease jet / Method: injection
Serial crystallography sample delivery injectionCarrier solvent: Superlube

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Processing

Software
NameVersionClassification
CrystFELdata reduction
CrystFEL0.6.3data scaling
PHASER2.5.7phasing
REFMAC5.8.0135refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5K5B

5k5b


Resolution: 2.21→36.94 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.968 / SU B: 17.135 / SU ML: 0.358 / SU R Cruickshank DPI: 0.3423 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.342 / ESU R Free: 0.235
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2562 1829 5.2 %RANDOM
Rwork0.2304 ---
obs0.2317 33150 90.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 162.04 Å2 / Biso mean: 78.626 Å2 / Biso min: 42.6 Å2
Baniso -1Baniso -2Baniso -3
1--0.33 Å20 Å2-0 Å2
2---0.99 Å2-0 Å2
3---1.32 Å2
Refinement stepCycle: final / Resolution: 2.21→36.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4794 0 86 147 5027
Biso mean--83.59 74.34 -
Num. residues----628
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0195136
X-RAY DIFFRACTIONr_bond_other_d0.0010.024921
X-RAY DIFFRACTIONr_angle_refined_deg1.15227056
X-RAY DIFFRACTIONr_angle_other_deg0.899311298
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8465648
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.6823.255212
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.06715760
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.4541538
X-RAY DIFFRACTIONr_chiral_restr0.0610.2796
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215868
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021144
LS refinement shellResolution: 2.21→2.267 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.443 96 -
Rwork0.411 1787 -
all-1883 -
obs--67.18 %

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