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- PDB-3is2: 2.3 Angstrom Crystal Structure of a Cys71 Sulfenic Acid form of Vivid -

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Basic information

Entry
Database: PDB / ID: 3is2
Title2.3 Angstrom Crystal Structure of a Cys71 Sulfenic Acid form of Vivid
Components(Vivid PAS protein VVD) x 2
KeywordsSIGNALING PROTEIN / Photoreceptor / Circadian Clock / Flavin / Sulfenic Acid
Function / homology
Function and homology information


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: 2.3 Å
AuthorsZoltowski, B.D. / Lamb, J.S. / Pabit, S.A. / Li, L. / Pollack, L. / Crane, B.R.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Illuminating solution responses of a LOV domain protein with photocoupled small-angle X-ray scattering.
Authors: Lamb, J.S. / Zoltowski, B.D. / Pabit, S.A. / Li, L. / Crane, B.R. / Pollack, L.
History
DepositionAug 25, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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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)36,6134
Polymers35,0422
Non-polymers1,5712
Water6,539363
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3760 Å2
ΔGint-31 kcal/mol
Surface area15390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.420, 81.110, 58.030
Angle α, β, γ (deg.)90.00, 95.03, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe crystal structure contains a dimer in the asymmetric unit, however the physiologically relevant photo-induced dimer is currently unknown.

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Components

#1: Protein Vivid PAS protein VVD


Mass: 17529.004 Da / Num. of mol.: 1 / Fragment: VVD-36 (UNP RESIDUES 37-186)
Source method: isolated from a genetically manipulated source
Details: CSO at position 71 / 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: Protein Vivid PAS protein VVD


Mass: 17513.004 Da / Num. of mol.: 1 / Fragment: VVD-36 (UNP RESIDUES 37-186)
Source method: isolated from a genetically manipulated source
Details: CYS at position 71 / Source: (gene. exp.) Neurospora crassa (fungus) / Gene: G17A4.050, Vivid, vvd / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9C3Y6
#3: 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
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 363 / 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: 2.44 Å3/Da / Density % sol: 49.52 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 20 mM imidazole, 26% PEG 4000, 100 mM trisodium citrate, 100 mM NaCl, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F3 / Wavelength: 1.28 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 20, 2007
RadiationMonochromator: Double-bounce downward, offset 25 -110 mm / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 15003 / Num. obs: 14822 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 33.5 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 24.3
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 6 / % possible all: 98.3

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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 / Resolution: 2.3→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.254 1504 -Random
Rwork0.226 ---
all0.254 15003 --
obs0.254 14822 98.8 %-
Refinement stepCycle: LAST / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2380 0 106 363 2849

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