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- PDB-3hji: 1.8 Angstrom Crystal Structure of the I74V:I85V Variant of Vivid ... -

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Basic information

Entry
Database: PDB / ID: 3hji
Title1.8 Angstrom Crystal Structure of the I74V:I85V Variant of Vivid (VVD).
ComponentsVivid PAS protein VVD
KeywordsSIGNALING PROTEIN / Photoreceptor / Circadian Clock / LOV / FAD
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: 1.8 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 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Oct 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 1.4Sep 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)36,5414
Polymers34,9702
Non-polymers1,5712
Water6,287349
1
A: Vivid PAS protein VVD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2702
Polymers17,4851
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Vivid PAS protein VVD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2702
Polymers17,4851
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3340 Å2
ΔGint-26 kcal/mol
Surface area15050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.4, 80.6, 57.4
Angle α, β, γ (deg.)90, 95.8, 90
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: 17484.949 Da / Num. of mol.: 2 / Mutation: I74V, I85V
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 / 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 / Water


Mass: 18.015 Da / Num. of mol.: 349 / 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: 2.47 Å3/Da / Density % sol: 50.16 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 3.6 mg/ml protein in buffer containing 5 mM DTT, 100 mM NaCl, 50 mM Hepes pH 8.0 and 10% glycerol combined with equal volume of 28% PEG 4k, 100 mM ammonium acetate, and 100 mM tri-sodium ...Details: 3.6 mg/ml protein in buffer containing 5 mM DTT, 100 mM NaCl, 50 mM Hepes pH 8.0 and 10% glycerol combined with equal volume of 28% PEG 4k, 100 mM ammonium acetate, and 100 mM tri-sodium 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: 1.76→46.6 Å / Num. all: 29885 / Num. obs: 29885 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 29.9 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 31
Reflection shellResolution: 1.76→1.83 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.474 / Mean I/σ(I) obs: 2.5 / Num. unique all: 3502 / % possible all: 96.6

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Processing

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

2pd7


Resolution: 1.8→30 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.266 2982 -random
Rwork0.244 ---
all0.266 30562 --
obs0.266 29885 97.8 %-
Displacement parametersBiso mean: 29.9 Å2
Refinement stepCycle: LAST / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2303 0 106 349 2758

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