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- PDB-2pd8: 1.8 Angstrom Crystal Structure of the Cys71Ser mutant of Vivid -

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Basic information

Entry
Database: PDB / ID: 2pd8
Title1.8 Angstrom Crystal Structure of the Cys71Ser mutant of Vivid
ComponentsVivid PAS protein VVD
KeywordsCIRCADIAN CLOCK PROTEIN / LOV Domain / flavin / photoreceptor / circadian clock
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. / Crane, B.R. / Bilwes, A.M.
CitationJournal: Science / Year: 2007
Title: Conformational switching in the fungal light sensor Vivid
Authors: Zoltowski, B.D. / Schwerdtfeger, C. / Widom, J. / Loros, J.J. / Bilwes, A.M. / Dunlap, J.C. / Crane, B.R.
History
DepositionMar 31, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 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 1.4Aug 30, 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)35,5404
Polymers33,9692
Non-polymers1,5712
Water6,720373
1
A: Vivid PAS protein VVD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,7702
Polymers16,9841
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)17,7702
Polymers16,9841
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.320, 80.590, 57.650
Angle α, β, γ (deg.)90.000, 95.600, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Vivid PAS protein VVD / Hypothetical protein NCU03967.1


Mass: 16984.443 Da / Num. of mol.: 2 / Fragment: residues 37-184 / Mutation: C71S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neurospora crassa (fungus) / Gene: vvd, G17A4.050 / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / 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.: 373 / 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: 50.22 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 30% PEG 5000 MME, 0.1M tri-sodium citrate, 0.1M Ammonium acetate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 10, 2006
RadiationMonochromator: Double-bounce downward, offset 25.4 mm / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 54748 / Num. obs: 54748 / % possible obs: 90.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.7 % / Biso Wilson estimate: 20.3 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 21.64
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.286 / Mean I/σ(I) obs: 2.81 / Num. unique all: 3636 / % possible all: 60

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT2data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2PD7

2pd7


Resolution: 1.8→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.284 2878 9.4 %Random
Rwork0.262 ---
all0.27 28834 --
obs0.27 28834 94.1 %-
Solvent computationBsol: 26.453 Å2
Displacement parametersBiso mean: 29.899 Å2
Baniso -1Baniso -2Baniso -3
1--8.405 Å20 Å213.4 Å2
2--12.447 Å20 Å2
3----4.042 Å2
Refinement stepCycle: LAST / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2311 0 106 373 2790
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_mcbond_it1.1761.5
X-RAY DIFFRACTIONc_scbond_it1.7912
X-RAY DIFFRACTIONc_mcangle_it1.8122
X-RAY DIFFRACTIONc_scangle_it2.6682.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2fad.par
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION4CNS_TOPPAR:ion.param

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