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- PDB-2pdr: 1.7 Angstrom Crystal Structure of the Photo-excited Blue-light Ph... -

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Basic information

Entry
Database: PDB / ID: 2pdr
Title1.7 Angstrom Crystal Structure of the Photo-excited Blue-light Photoreceptor 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: 1.7 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
DepositionApr 1, 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 1.3Aug 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_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
C: Vivid PAS protein VVD
D: Vivid PAS protein VVD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,1448
Polymers68,0024
Non-polymers3,1424
Water9,008500
1
A: Vivid PAS protein VVD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,7862
Polymers17,0011
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)17,7862
Polymers17,0011
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Vivid PAS protein VVD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,7862
Polymers17,0011
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Vivid PAS protein VVD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,7862
Polymers17,0011
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.970, 81.130, 64.730
Angle α, β, γ (deg.)90.00, 89.94, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 17000.510 Da / Num. of mol.: 4 / 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.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 500 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 4

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Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 49.39 %
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

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31001
41001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X29A11.1
SYNCHROTRONNSLS X29A21.1
SYNCHROTRONNSLS X29A31.1
SYNCHROTRONNSLS X29A41.1
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDMar 13, 2006
ADSC QUANTUM 3152CCDMar 13, 2006
ADSC QUANTUM 3153CCDMar 13, 2006
ADSC QUANTUM 3154CCDMar 13, 2006
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Cryogenically cooled double crystal monochrometer with horizontal focusing sagittal bend second mono crystal with 4:1 magnification ratio and vertically focusing mirror.SINGLE WAVELENGTHMx-ray1
2Cryogenically cooled double crystal monochrometer with horizontal focusing sagittal bend second mono crystal with 4:1 magnification ratio and vertically focusing mirror.SINGLE WAVELENGTHMx-ray1
3Cryogenically cooled double crystal monochrometer with horizontal focusing sagittal bend second mono crystal with 4:1 magnification ratio and vertically focusing mirror.SINGLE WAVELENGTHMx-ray1
4Cryogenically cooled double crystal monochrometer with horizontal focusing sagittal bend second mono crystal with 4:1 magnification ratio and vertically focusing mirror.SINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. all: 59234 / Num. obs: 59234 / % possible obs: 82.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.1 % / Biso Wilson estimate: 18.3 Å2 / Rmerge(I) obs: 0.102 / Net I/σ(I): 13.31
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.431 / Mean I/σ(I) obs: 1.91 / Num. unique all: 4525 / % possible all: 63.6

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Processing

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

2pd7


Resolution: 1.7→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.249 6000 -Random
Rwork0.226 ---
all0.23 59190 --
obs0.23 59190 82.7 %-
Refinement stepCycle: LAST / Resolution: 1.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4988 0 424 500 5912
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_angle_deg
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_mcbond_it0.9191.5
X-RAY DIFFRACTIONc_mcangle_it1.4652
X-RAY DIFFRACTIONc_scbond_it1.5072
X-RAY DIFFRACTIONc_scangle_it2.2062.5

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