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- PDB-1g28: STRUCTURE OF A FLAVIN-BINDING DOMAIN, LOV2, FROM THE CHIMERIC PHY... -

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Basic information

Entry
Database: PDB / ID: 1g28
TitleSTRUCTURE OF A FLAVIN-BINDING DOMAIN, LOV2, FROM THE CHIMERIC PHYTOCHROME/PHOTOTROPIN PHOTORECEPTOR PHY3
ComponentsPHY3 PROTEIN
KeywordsSIGNALING PROTEIN / ELECTRON TRANSPORT / phototropin / LOV / PAS fold / photoreceptor / flavoprotein / FMN-binding domain / alpha-beta structure
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 / Phytochrome, central region / PAS fold-2 / PAS fold / 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 / Phytochrome, central region / PAS fold-2 / PAS fold / 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 / MOLECULAR REPLACEMENT / Resolution: 2.73 Å
AuthorsCrosson, S. / Moffat, K.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2001
Title: Structure of a flavin-binding plant photoreceptor domain: insights into light-mediated signal transduction
Authors: Crosson, S. / Moffat, K.
History
DepositionOct 17, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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
Water91951
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)44.890, 54.078, 70.619
Angle α, β, γ (deg.)93.32, 94.01, 90.06
Int Tables number1
Cell settingtriclinic
Space group name H-MP1

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Components

#1: Protein
PHY3 PROTEIN


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
Source: (gene. exp.) Adiantum capillus-veneris (maidenhair fern)
Gene: PHY3 / Plasmid: PCAL-NEK / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / 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.: 51 / 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: 3.5 Å3/Da / Density % sol: 64.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 5000 MME, Tris, glycerol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
150 mMTris-HCl1reservoir
224 %(w/v)mPEG50001reservoir
312 %(v/v)glycerol1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Apr 24, 2000 / Details: mirrors
RadiationMonochromator: Cu-K-alpha / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.73→35.16 Å / Num. all: 17568 / Num. obs: 16249 / % possible obs: 92.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 1.8 % / Biso Wilson estimate: 20.5 Å2 / Rmerge(I) obs: 0.115 / Net I/σ(I): 14.3
Reflection shellResolution: 2.73→2.9 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.443 / % possible all: 86.1
Reflection shell
*PLUS
% possible obs: 86.1 %

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.73→35.16 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 368490.28 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.272 1179 7.3 %SHELLS
Rwork0.247 ---
all0.251 17568 --
obs0.247 16249 92.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 51.79 Å2 / ksol: 0.36 e/Å3
Displacement parametersBiso mean: 34.2 Å2
Baniso -1Baniso -2Baniso -3
1-6.96 Å216.18 Å2-0.06 Å2
2---1.36 Å25.16 Å2
3----5.59 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.41 Å
Luzzati d res low-5 Å
Luzzati sigma a0.92 Å0.93 Å
Refinement stepCycle: LAST / Resolution: 2.73→35.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3276 0 124 51 3451
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d24.2
X-RAY DIFFRACTIONc_improper_angle_d0.67
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.73→2.9 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.42 176 7 %
Rwork0.425 2344 -
obs--86 %
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.67

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