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- PDB-3hjk: 2.0 Angstrom Structure of the Ile74Val Variant of Vivid (VVD). -

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Basic information

Entry
Database: PDB / ID: 3hjk
Title2.0 Angstrom Structure of the Ile74Val Variant of Vivid (VVD).
ComponentsVivid PAS protein VVD
KeywordsSIGNALING PROTEIN / Photoreceptor / Circadian Clock / FAD / LOV / PAS
Function / homology
Function and homology information


nucleotide binding / nucleus
Similarity search - Function
PAS domain / PAS domain / Beta-Lactamase / PAS repeat profile. / PAS domain / PAS domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Vivid PAS protein VVD
Similarity search - Component
Biological speciesNeurospora crassa (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsZoltowski, B.D. / Vaccaro, B.J. / Crane, B.R.
CitationJournal: Nat.Chem.Biol. / Year: 2009
Title: Mechanism-based tuning of a LOV domain photoreceptor.
Authors: Zoltowski, B.D. / Vaccaro, B. / Crane, B.R.
History
DepositionMay 21, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 29, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Vivid PAS protein VVD
B: Vivid PAS protein VVD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,5694
Polymers34,9982
Non-polymers1,5712
Water5,621312
1
A: Vivid PAS protein VVD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2852
Polymers17,4991
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Vivid PAS protein VVD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2852
Polymers17,4991
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.780, 80.300, 56.900
Angle α, β, γ (deg.)90.00, 94.76, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe protein in monomeric, however following photo-excitation the protein dimerizes. The biological dimer structure is currently unknown.

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Components

#1: Protein Vivid PAS protein VVD


Mass: 17498.977 Da / Num. of mol.: 2 / Mutation: I74V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neurospora crassa (fungus) / Gene: G17A4.050, Vivid, vvd / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9C3Y6
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 312 / 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: 2.37 Å3/Da / Density % sol: 48.01 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: Protein at 3.6 mg/ml dissolved in Buffer containing 5 mM DTT, 100 mM NaCl, 50 mM HEPES pH 8.0 and 10% glycerol is combined with an equal volume of 28% PEG 4k, 100 mM ammonium acetate, 100 mM ...Details: Protein at 3.6 mg/ml dissolved in Buffer containing 5 mM DTT, 100 mM NaCl, 50 mM HEPES pH 8.0 and 10% glycerol is combined with an equal volume of 28% PEG 4k, 100 mM ammonium acetate, 100 mM trisodium citrate pH 5.6., VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 1, 2008
RadiationMonochromator: Double-bounce downward, offset 25.4 mm / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→35.66 Å / Num. all: 21712 / Num. obs: 21712 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 4.5 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 29
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.349 / Mean I/σ(I) obs: 4.5 / Num. unique all: 1903 / % possible all: 93.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2pd7

2pd7


Resolution: 2→30 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.261 2117 -Random
Rwork0.244 ---
all0.261 21712 --
obs0.261 21549 99.2 %-
Displacement parametersBiso max: 100.24 Å2 / Biso mean: 33.546 Å2 / Biso min: 10.37 Å2
Baniso -1Baniso -2Baniso -3
1--3.492 Å20 Å27.137 Å2
2--10.768 Å20 Å2
3----7.276 Å2
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2323 0 106 312 2741
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.2121.5
X-RAY DIFFRACTIONc_scbond_it1.8092
X-RAY DIFFRACTIONc_mcangle_it2.0042
X-RAY DIFFRACTIONc_scangle_it2.7312.5

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