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- PDB-6ptz: Crystal structure of pigeon Cryptochrome 4 mutant Y319D in comple... -

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Basic information

Entry
Database: PDB / ID: 6ptz
TitleCrystal structure of pigeon Cryptochrome 4 mutant Y319D in complex with flavin adenine dinucleotide
ComponentsCryptochrome-1
KeywordsCIRCADIAN CLOCK PROTEIN / Magnetosensor / photolyase
Function / homology
Function and homology information


DNA Cyclobutane Dipyrimidine Photolyase, subunit A; domain 3 / DNA Cyclobutane Dipyrimidine Photolyase, subunit A, domain 3 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #80 / Cryptochrome/DNA photolyase class 1 / Cryptochrome/DNA photolyase, FAD-binding domain / FAD binding domain of DNA photolyase / DNA photolyase, N-terminal / Cryptochrome/photolyase, N-terminal domain superfamily / DNA photolyase / Photolyase/cryptochrome alpha/beta domain profile. ...DNA Cyclobutane Dipyrimidine Photolyase, subunit A; domain 3 / DNA Cyclobutane Dipyrimidine Photolyase, subunit A, domain 3 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #80 / Cryptochrome/DNA photolyase class 1 / Cryptochrome/DNA photolyase, FAD-binding domain / FAD binding domain of DNA photolyase / DNA photolyase, N-terminal / Cryptochrome/photolyase, N-terminal domain superfamily / DNA photolyase / Photolyase/cryptochrome alpha/beta domain profile. / Cryptochrome/DNA photolyase, FAD-binding domain-like superfamily / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / DI(HYDROXYETHYL)ETHER / Cryptochrome-1
Similarity search - Component
Biological speciesColumba livia (rock pigeon)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.793 Å
AuthorsZoltowski, B.D. / Chelliah, Y. / Wickramaratne, A.C. / Jarocha, L. / Karki, N. / Mouritsen, H. / Hore, P.J. / Hibbs, R.E. / Green, C.B. / Takahashi, J.S.
Funding support United States, European Union, Germany, 10items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB-1613643 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)NS095899 United States
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)DA042072 United States
European Research Council (ERC)340451European Union
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM090247 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM112991 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM127122 United States
German Research Foundation (DFG)SFB 1372 Germany
German Research Foundation (DFG)GRK 1885 Germany
Other governmentFA9550-14-1-0095 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2019
Title: Chemical and structural analysis of a photoactive vertebrate cryptochrome from pigeon.
Authors: Zoltowski, B.D. / Chelliah, Y. / Wickramaratne, A. / Jarocha, L. / Karki, N. / Xu, W. / Mouritsen, H. / Hore, P.J. / Hibbs, R.E. / Green, C.B. / Takahashi, J.S.
History
DepositionJul 16, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 18, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Oct 9, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support
Item: _pdbx_audit_support.country / _pdbx_audit_support.funding_organization
Revision 1.4Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cryptochrome-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,77811
Polymers58,1331
Non-polymers1,64510
Water7,278404
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.733, 85.574, 103.283
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Cryptochrome-1 /


Mass: 58133.277 Da / Num. of mol.: 1 / Mutation: Y319D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Columba livia (rock pigeon) / Gene: A306_00007326 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A2I0LZR8

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Non-polymers , 5 types, 414 molecules

#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 404 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.13 Å3/Da / Density % sol: 42.26 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, hanging drop
Details: Crystals were obtained at 21C in dark from a 1:1 mixture of protein (10-12 mg/mL) and a reservoir solution consisting of 7.5% PEG 6000 and 0.1 M HEPES pH 7.1. Crystal reached maximum size ...Details: Crystals were obtained at 21C in dark from a 1:1 mixture of protein (10-12 mg/mL) and a reservoir solution consisting of 7.5% PEG 6000 and 0.1 M HEPES pH 7.1. Crystal reached maximum size after 4-5 days and were harvested at that time in the dark. Crystals were transferred to cryoprotectant solution consisting of 5% PEG 6000, 0.1 M HEPES pH 7, 2 mM DTT and either 30% P400 or 30% glycerol. Crystals were flash-frozen in liquid nitrogen in the dark

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.793→50 Å / Num. obs: 38744 / % possible obs: 85.3 % / Redundancy: 4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.077 / Net I/σ(I): 32.1
Reflection shellResolution: 1.793→1.86 Å / Rmerge(I) obs: 0.389 / Num. unique obs: 38705 / CC1/2: 0.883

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4K0R

4k0r


Resolution: 1.793→44.214 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.06
RfactorNum. reflection% reflection
Rfree0.2061 2000 5.17 %
Rwork0.1629 --
obs0.1652 38708 85.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 69.53 Å2 / Biso mean: 24.5508 Å2 / Biso min: 8.04 Å2
Refinement stepCycle: final / Resolution: 1.793→44.214 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3930 0 109 404 4443
Biso mean--29.34 38.19 -
Num. residues----479
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074158
X-RAY DIFFRACTIONf_angle_d0.8955630
X-RAY DIFFRACTIONf_chiral_restr0.054588
X-RAY DIFFRACTIONf_plane_restr0.006714
X-RAY DIFFRACTIONf_dihedral_angle_d16.3642442
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.793-1.83750.22121280.1848235078
1.8375-1.88720.25781410.1816257585
1.8872-1.94270.2491470.1784272489
1.9427-2.00540.21581490.1757271790
2.0054-2.07710.23971470.1719270389
2.0771-2.16030.20581480.1636271389
2.1603-2.25860.20031460.161268488
2.2586-2.37770.20331450.1584266788
2.3777-2.52660.18091470.1502268987
2.5266-2.72170.19931430.1533262486
2.7217-2.99550.21221420.1628261184
2.9955-3.42880.21571400.1563257183
3.4288-4.31940.19631380.1458254081
4.3194-44.2140.18651390.1809254077
Refinement TLS params.Method: refined / Origin x: -7.4524 Å / Origin y: 13.8059 Å / Origin z: -28.5187 Å
111213212223313233
T0.0797 Å20.0001 Å20.0198 Å2-0.0721 Å20.0103 Å2--0.1631 Å2
L0.4728 °20.2404 °20.5312 °2-0.5306 °20.2813 °2--2.0757 °2
S0.0257 Å °-0.0265 Å °0.0182 Å °0.0854 Å °-0.0466 Å °0.0222 Å °0.0009 Å °-0.0174 Å °0.0231 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 497
2X-RAY DIFFRACTION1allB1
3X-RAY DIFFRACTION1allC1
4X-RAY DIFFRACTION1allS1 - 418
5X-RAY DIFFRACTION1allS419
6X-RAY DIFFRACTION1allF1
7X-RAY DIFFRACTION1allF2 - 6
8X-RAY DIFFRACTION1allF7
9X-RAY DIFFRACTION1allD2

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