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- PDB-1n9l: Crystal structure of the Phot-LOV1 domain from Chlamydomonas rein... -

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Basic information

Entry
Database: PDB / ID: 1n9l
TitleCrystal structure of the Phot-LOV1 domain from Chlamydomonas reinhardtii in the dark state.
Componentsputative blue light receptor
KeywordsELECTRON TRANSPORT / phototropin / flavin
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 / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 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) / PAS domain / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / Beta-Lactamase / 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) / PAS domain / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / Beta-Lactamase / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / Phototropin / Phototropin
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsFedorov, R. / Schlichting, I. / Hartmann, E. / Domratcheva, T. / Fuhrmann, M. / Hegemann, P.
CitationJournal: Biophys.J. / Year: 2003
Title: Crystal structures and molecular mechanism of a light-induced signaling switch: The Phot-LOV1 domain from Chlamydomonas reinhardtii.
Authors: Fedorov, R. / Schlichting, I. / Hartmann, E. / Domratcheva, T. / Fuhrmann, M. / Hegemann, P.
History
DepositionNov 25, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 17, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Nov 6, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.title
Revision 1.5Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: putative blue light receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,5423
Polymers11,9901
Non-polymers5522
Water1,946108
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: putative blue light receptor
hetero molecules

A: putative blue light receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0846
Polymers23,9792
Non-polymers1,1054
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_666-y+1,-x+1,-z+7/61
Buried area2980 Å2
ΔGint-56 kcal/mol
Surface area11630 Å2
MethodPISA
3
A: putative blue light receptor
hetero molecules

A: putative blue light receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0846
Polymers23,9792
Non-polymers1,1054
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z+2/31
Buried area3440 Å2
ΔGint-25 kcal/mol
Surface area10800 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)122.100, 122.100, 46.100
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-900-

SO4

21A-677-

HOH

31A-678-

HOH

41A-689-

HOH

51A-818-

HOH

61A-822-

HOH

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Components

#1: Protein putative blue light receptor / Phot-LOV1


Mass: 11989.646 Da / Num. of mol.: 1 / Fragment: residues 17-125
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Plasmid: pET16 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q8LPE0, UniProt: Q8LPD9*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / 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: 3.59 Å3/Da / Density % sol: 65.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: HEPES, ammonium sulfate, PEG8000, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110.5 mg/mlprotein1drop
210 mMsodium phosphate1drop
310 mM1droppH8.0NaCl
4100 mMsodium HEPES1reservoirpH7.3
51.5-1.8 Mammonium sulfate1reservoir
61-8 %PEG80001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 1, 2002
RadiationMonochromator: Si111 or Si311 crystals, LN2 cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9393 Å / Relative weight: 1
ReflectionResolution: 1.9→15 Å / Num. all: 16467 / Num. obs: 16142 / % possible obs: 98 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.8 % / Biso Wilson estimate: 32.7 Å2 / Rsym value: 0.068 / Net I/σ(I): 12.8
Reflection shellResolution: 1.9→1.97 Å / Mean I/σ(I) obs: 3.5 / Rsym value: 0.351 / % possible all: 96.6
Reflection
*PLUS
Num. measured all: 77830 / Rmerge(I) obs: 0.068
Reflection shell
*PLUS
% possible obs: 96.6 % / Rmerge(I) obs: 0.351

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Processing

Software
NameVersionClassification
ProDCdata collection
XDSdata reduction
AMoREphasing
CNS1refinement
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1G28

1g28


Resolution: 1.9→15 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.248 804 RANDOM
Rwork0.232 --
all0.233 16142 -
obs0.233 16142 -
Refinement stepCycle: LAST / Resolution: 1.9→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms842 0 36 108 986
Refinement
*PLUS
% reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONbond_d0.008
X-RAY DIFFRACTIONangle_d
X-RAY DIFFRACTIONangle_deg1.28

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