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- PDB-1jnu: Photoexcited structure of the plant photoreceptor domain, phy3 LOV2 -

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Basic information

Entry
Database: PDB / ID: 1jnu
TitlePhotoexcited structure of the plant photoreceptor domain, phy3 LOV2
ComponentsPHY3 PROTEIN
KeywordsSIGNALING PROTEIN / ELECTRON TRANSPORT / cysteinyl-flavin adduct / photoexcited / PAS / LOV / plant photoreceptor / phototropin / photochemistry / light-driven bond / phy3
Function / homology
Function and homology information


blue light photoreceptor activity / detection of visible light / non-specific serine/threonine protein kinase / protein serine/threonine kinase activity / regulation of DNA-templated transcription / ATP binding
Similarity search - Function
Phytochrome chromophore binding site / Phytochrome chromophore attachment site signature. / Phytochrome / Phytochrome, PHY domain superfamily / PAS fold-2 / PAS fold / Phytochrome, central region / Phytochrome region / Phytochrome chromophore attachment domain / Phytochrome chromophore attachment site domain profile. ...Phytochrome chromophore binding site / Phytochrome chromophore attachment site signature. / Phytochrome / Phytochrome, PHY domain superfamily / PAS fold-2 / PAS fold / Phytochrome, central region / Phytochrome region / Phytochrome chromophore attachment domain / Phytochrome chromophore attachment site domain profile. / 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 / GAF domain / Domain present in phytochromes and cGMP-specific phosphodiesterases. / GAF domain / GAF-like domain superfamily / 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, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / non-specific serine/threonine protein kinase
Similarity search - Component
Biological speciesAdiantum capillus-veneris (maidenhair fern)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsCrosson, S. / Moffat, K.
CitationJournal: Plant Cell / Year: 2002
Title: Photoexcited structure of a plant photoreceptor domain reveals a light-driven molecular switch.
Authors: Crosson, S. / Moffat, K.
History
DepositionJul 25, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 14, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 3, 2024Group: 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_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PHY3 PROTEIN
B: PHY3 PROTEIN
C: PHY3 PROTEIN
D: PHY3 PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,5528
Polymers48,7274
Non-polymers1,8254
Water1,17165
1
A: PHY3 PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,6382
Polymers12,1821
Non-polymers4561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PHY3 PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,6382
Polymers12,1821
Non-polymers4561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: PHY3 PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,6382
Polymers12,1821
Non-polymers4561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: PHY3 PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,6382
Polymers12,1821
Non-polymers4561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.843, 54.771, 70.963
Angle α, β, γ (deg.)93.14, 93.79, 90.40
Int Tables number1
Cell settingtriclinic
Space group name H-MP1

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Components

#1: Protein
PHY3 PROTEIN / phy3 LOV2


Mass: 12181.764 Da / Num. of mol.: 4
Fragment: FMN-BINDING DOMAIN OF CHIMERIC PHYTOCHROME/PHOTOTROPIN PHOTORECEPTOR, LOV3
Source method: isolated from a genetically manipulated source
Details: contains a cysteinyl-flavin C(4a) covalent adduct
Source: (gene. exp.) Adiantum capillus-veneris (maidenhair fern)
Gene: phy3 / Plasmid: pcal-n-ek / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-DE3 / References: UniProt: Q9ZWQ6
#2: Chemical
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


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


Mass: 18.015 Da / Num. of mol.: 65 / Source method: isolated from a natural source / Formula: H2O
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: 3.56 Å3/Da / Density % sol: 65.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 5000 MME, Tris, Glycerol, pH 8.0, VAPOR DIFFUSION, HANGING DROP at 293K
Crystal grow
*PLUS
Temperature: 25 ℃ / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
122 %PEG5000 MME11
212 %glycerol11
350 mMTris11pH8.0
415 mg/mlprotein12

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Data collection

DiffractionMean temperature: 296 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 5, 2001
RadiationMonochromator: Silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→26.8 Å / Num. all: 29191 / Num. obs: 17700 / % possible obs: 87.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 1.65 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 12.3
Reflection shellResolution: 2.6→2.69 Å / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 3.2 / Num. unique all: 1583 / % possible all: 79
Reflection
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 30 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.044
Reflection shell
*PLUS
% possible obs: 79 % / Rmerge(I) obs: 0.19

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Processing

Software
NameClassification
EPMRphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: phy3 LOV2 dark-state structure

Resolution: 2.6→26.8 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.25914 1295 7.9 %RESOLUTION SHELL
Rwork0.23574 ---
all0.23758 29191 --
obs0.23758 17700 87.5 %-
Displacement parametersBiso mean: 32.69 Å2
Baniso -1Baniso -2Baniso -3
1-4.36 Å28.16 Å21.06 Å2
2--0.62 Å20.9 Å2
3----4.62 Å2
Refinement stepCycle: LAST / Resolution: 2.6→26.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3276 0 124 65 3465
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.011.5
X-RAY DIFFRACTIONp_angle_d1.42
X-RAY DIFFRACTIONp_mcbond_it1.9791.5
X-RAY DIFFRACTIONp_mcangle_it3.592
X-RAY DIFFRACTIONp_scbond_it2.6793
X-RAY DIFFRACTIONp_scangle_it4.2114.5
Refinement
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 30 Å / % reflection Rfree: 7.3 % / Rfactor obs: 0.238 / Rfactor Rfree: 0.259 / Rfactor Rwork: 0.238
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 32.7 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.01
X-RAY DIFFRACTIONp_angle_d1.36

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