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- PDB-8qi8: Cryogenic temperature dark state structure of CrPhotLOV1 -

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Basic information

Entry
Database: PDB / ID: 8qi8
TitleCryogenic temperature dark state structure of CrPhotLOV1
ComponentsPhototropin
KeywordsFLAVOPROTEIN / PHOTOTROPIN / FLAVIN / ELECTRON TRANSPORT
Function / homology
Function and homology information


blue light signaling pathway / blue light photoreceptor activity / protein autophosphorylation / 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: 1.35 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 11, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phototropin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,3182
Polymers12,8621
Non-polymers4561
Water3,261181
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area870 Å2
ΔGint-5 kcal/mol
Surface area6350 Å2
2
A: Phototropin
hetero molecules

A: Phototropin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6364
Polymers25,7232
Non-polymers9132
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z+2/31
Buried area3440 Å2
ΔGint-25 kcal/mol
Surface area11000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.090, 121.090, 46.040
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-771-

HOH

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Components

#1: Protein Phototropin


Mass: 12861.666 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: PHOT / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8LPD9
#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.: 181 / 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

Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100 mM Na cacodylate pH6.5 1 M Na citrate dibasic trihydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.35→39.64 Å / Num. obs: 43943 / % possible obs: 99.43 % / Redundancy: 19.29 % / Biso Wilson estimate: 20.41 Å2 / CC1/2: 1 / CC star: 1 / Rrim(I) all: 0.052 / Net I/σ(I): 30.1
Reflection shellResolution: 1.35→1.4 Å / Num. unique obs: 4076 / CC1/2: 0.74 / CC star: 0.92 / Rrim(I) all: 2.239

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Processing

Software
NameVersionClassification
PHENIX1.20_4459refinement
PHASERphasing
XDSdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.35→39.64 Å / SU ML: 0.1475 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.0475
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1482 4094 4.97 %
Rwork0.1258 78242 -
obs0.1268 43696 99.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.69 Å2
Refinement stepCycle: LAST / Resolution: 1.35→39.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms844 0 31 181 1056
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088975
X-RAY DIFFRACTIONf_angle_d1.14111348
X-RAY DIFFRACTIONf_chiral_restr0.087152
X-RAY DIFFRACTIONf_plane_restr0.0116171
X-RAY DIFFRACTIONf_dihedral_angle_d20.1066150
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.370.35011190.3452271X-RAY DIFFRACTION84.15
1.37-1.380.3231400.3232713X-RAY DIFFRACTION99.65
1.38-1.40.27421430.28042702X-RAY DIFFRACTION99.89
1.4-1.420.29551440.26882718X-RAY DIFFRACTION99.86
1.42-1.440.28961400.24372734X-RAY DIFFRACTION99.93
1.44-1.460.28391390.22882710X-RAY DIFFRACTION100
1.46-1.480.24281430.22122684X-RAY DIFFRACTION99.93
1.48-1.50.27241390.21232723X-RAY DIFFRACTION100
1.5-1.530.21571430.20342720X-RAY DIFFRACTION99.93
1.53-1.560.22511430.2072693X-RAY DIFFRACTION100
1.56-1.580.24121430.17992715X-RAY DIFFRACTION100
1.58-1.610.18651440.16492713X-RAY DIFFRACTION99.86
1.61-1.650.19521360.14872717X-RAY DIFFRACTION99.96
1.65-1.680.16391420.13792717X-RAY DIFFRACTION100
1.68-1.720.1581450.12832720X-RAY DIFFRACTION100
1.72-1.770.15721430.11842689X-RAY DIFFRACTION99.96
1.77-1.810.13721360.1182711X-RAY DIFFRACTION99.89
1.81-1.870.14321370.10912728X-RAY DIFFRACTION100
1.87-1.930.13891440.11132744X-RAY DIFFRACTION100
1.93-20.12251440.10552704X-RAY DIFFRACTION100
2-2.080.12431390.09662695X-RAY DIFFRACTION100
2.08-2.170.1221460.0972708X-RAY DIFFRACTION100
2.17-2.280.12631430.09832722X-RAY DIFFRACTION100
2.28-2.430.11741450.10282702X-RAY DIFFRACTION100
2.43-2.610.14231450.10462699X-RAY DIFFRACTION100
2.61-2.880.13321410.11582747X-RAY DIFFRACTION100
2.88-3.290.14541430.1112712X-RAY DIFFRACTION100
3.29-4.150.13131440.10482708X-RAY DIFFRACTION100
4.15-39.640.14111410.14432723X-RAY DIFFRACTION99.83

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