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- PDB-3d72: 1.65 Angstrom crystal structure of the Cys71Val variant in the fu... -

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Basic information

Entry
Database: PDB / ID: 3d72
Title1.65 Angstrom crystal structure of the Cys71Val variant in the fungal photoreceptor VVD
ComponentsVivid PAS protein VVD
KeywordsSIGNALING PROTEIN / Circadian / photoreceptor / blue-light / LOV / PAS / VVD
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 / Vivid PAS protein VVD
Similarity search - Component
Biological speciesNeurospora crassa (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsZoltowski, B.D. / Crane, B.R.
CitationJournal: Biochemistry / Year: 2008
Title: Light activation of the LOV protein vivid generates a rapidly exchanging dimer.
Authors: Zoltowski, B.D. / Crane, B.R.
History
DepositionMay 20, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 27, 2018Group: Data collection / Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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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)35,5644
Polymers33,9932
Non-polymers1,5712
Water8,323462
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1250 Å2
ΔGint-14 kcal/mol
Surface area15770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.240, 80.700, 57.580
Angle α, β, γ (deg.)90.00, 95.16, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Vivid PAS protein VVD


Mass: 16996.496 Da / Num. of mol.: 2 / Fragment: Fungal Photoreceptor VVD / Mutation: c71v
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neurospora crassa (fungus) / Gene: vvd, G17A4.050 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: Q9C3Y6, UniProt: Q1K5Y8*PLUS
#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.: 462 / 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: 50.14 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 26% PEG 4000, 100 mM triSodium Citrate pH 5.6, 100 mM Sodium Acetate, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9179 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 27, 2007
RadiationMonochromator: Horizontal bent Si(111), asymmetrically cut with water cooled Cu Block
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9179 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. all: 39657 / Num. obs: 39115 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 16.93 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 37.95
Reflection shellResolution: 1.65→1.71 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.18 / Mean I/σ(I) obs: 6.9 / Num. unique all: 3682 / % possible all: 94.1

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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: 1.65→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.26 3948 -Random
Rwork0.25 ---
all0.26 39657 --
obs0.26 39115 98.6 %-
Refinement stepCycle: LAST / Resolution: 1.65→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2376 0 106 462 2944
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.5

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