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- PDB-8qii: CrPhotLOV1 light state structure 27.5 ms (25-30 ms) after illumin... -

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Basic information

Entry
Database: PDB / ID: 8qii
TitleCrPhotLOV1 light state structure 27.5 ms (25-30 ms) after illumination determined by time-resolved serial synchrotron crystallography at room temperature
ComponentsPhototropin
KeywordsFLAVOPROTEIN / PHOTOTROPIN / FLAVIN / ELECTRON TRANSPORT
Function / homology
Function and homology information


blue light signaling pathway / blue light photoreceptor activity / protein autophosphorylation / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity ...blue light signaling pathway / blue light photoreceptor activity / protein autophosphorylation / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H3T6 kinase activity / histone H2AS1 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function
PAS domain / PAS-associated, C-terminal / PAC domain profile. / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / PAS domain / PAS repeat profile. / PAS domain ...PAS domain / PAS-associated, C-terminal / PAC domain profile. / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / Phototropin
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsGotthard, G. / Mous, S. / Weinert, T. / Maia, R.N.A. / James, D. / Dworkowski, F. / Gashi, D. / Antonia, F. / Wang, M. / Panepucci, E. ...Gotthard, G. / Mous, S. / Weinert, T. / Maia, R.N.A. / James, D. / Dworkowski, F. / Gashi, D. / Antonia, F. / Wang, M. / Panepucci, E. / Ozerov, D. / Schertler, G.F.X. / Heberle, J. / Standfuss, J. / Nogly, P.
Funding supportEuropean Union, Switzerland, Poland, 4items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European Commission701647European Union
Swiss National Science FoundationPZ00P3_174169 Switzerland
Polish National Science CentreUMO-2021/03/H/NZ1/00002 Poland
Swiss National Science Foundation192760 Switzerland
CitationJournal: Iucrj / Year: 2024
Title: Capturing the blue-light activated state of the Phot-LOV1 domain from Chlamydomonas reinhardtii using time-resolved serial synchrotron crystallography.
Authors: Gotthard, G. / Mous, S. / Weinert, T. / Maia, R.N.A. / James, D. / Dworkowski, F. / Gashi, D. / Furrer, A. / Ozerov, D. / Panepucci, E. / Wang, M. / Schertler, G.F.X. / Heberle, J. / Standfuss, J. / Nogly, P.
History
DepositionSep 12, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 24, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed ..._citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Sep 11, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phototropin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7952
Polymers15,3381
Non-polymers4561
Water68538
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area840 Å2
ΔGint-5 kcal/mol
Surface area6060 Å2
2
A: Phototropin
hetero molecules

A: Phototropin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5894
Polymers30,6772
Non-polymers9132
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z+2/31
Buried area3050 Å2
ΔGint-25 kcal/mol
Surface area10750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.540, 121.540, 46.180
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Space group name HallP652(x,y,z+1/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z+1/2
#9: y,x,-z+2/3
#10: -y,-x,-z+1/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+5/6
Components on special symmetry positions
IDModelComponents
11A-623-

HOH

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Components

#1: Protein Phototropin / Blue light receptor PHOT


Mass: 15338.354 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: PHOT, CHLRE_03g199000v5, CHLREDRAFT_183965 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q8LPD9, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 3.21 Å3/Da / Density % sol: 61.68 %
Crystal growTemperature: 293 K / Method: batch mode / pH: 6.5
Details: 100 mM sodium cacodylate at pH 6.5 and 1.0 M sodium citrate dibasic trihydrate

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.35→104.84 Å / Num. obs: 8744 / % possible obs: 100 % / Redundancy: 412.36 % / Biso Wilson estimate: 41.32 Å2 / CC1/2: 0.99 / CC star: 1 / R split: 0.1391 / Net I/σ(I): 6.51
Reflection shellResolution: 2.35→2.39 Å / Redundancy: 235 % / Mean I/σ(I) obs: 0.76 / Num. unique obs: 849 / CC1/2: 0.32 / CC star: 0.69 / R split: 1.2617 / % possible all: 100
Serial crystallography sample deliveryMethod: injection

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
CrystFELdata reduction
SCALEITdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→39.78 Å / SU ML: 0.4801 / Cross valid method: FREE R-VALUE / σ(F): 0.01 / Phase error: 31.7789
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2508 360 4.96 %
Rwork0.1979 6896 -
obs0.2004 7256 98.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.34 Å2
Refinement stepCycle: LAST / Resolution: 2.5→39.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms830 0 31 38 899
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084913
X-RAY DIFFRACTIONf_angle_d1.13531254
X-RAY DIFFRACTIONf_chiral_restr0.052140
X-RAY DIFFRACTIONf_plane_restr0.0083158
X-RAY DIFFRACTIONf_dihedral_angle_d19.4799340
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.860.431140.37042227X-RAY DIFFRACTION98.78
2.86-3.60.29631200.21292270X-RAY DIFFRACTION98.8
3.61-39.780.18851260.14312399X-RAY DIFFRACTION98.67

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