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- PDB-6pu0: Pigeon Cryptochrome4 bound to flavin adenine dinucleotide -

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Basic information

Entry
Database: PDB / ID: 6pu0
TitlePigeon Cryptochrome4 bound to 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 / TRIETHYLENE GLYCOL / Cryptochrome-1
Similarity search - Component
Biological speciesColumba livia (rock pigeon)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8979 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
Air Force Office of Scientific ResearchFA9550-14-1-0095 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)59,6969
Polymers58,1811
Non-polymers1,5148
Water5,783321
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.099, 86.578, 104.267
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Cryptochrome-1


Mass: 58181.363 Da / Num. of mol.: 1
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 , 6 types, 329 molecules

#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 321 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.19 Å3/Da / Density % sol: 43.74 %
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 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 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: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 6, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.849→104.073 Å / Num. obs: 41952 / % possible obs: 94.2 % / Redundancy: 3.4 % / Biso Wilson estimate: 16.1759252839 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.097 / Net I/σ(I): 13.5
Reflection shellResolution: 1.9→1.97 Å / Rmerge(I) obs: 0.438 / Num. unique obs: 37143 / CC1/2: 0.816

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Processing

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

4k0r


Resolution: 1.8979→48.0201133545 Å / SU ML: 0.168930378483 / Cross valid method: FREE R-VALUE / σ(F): 1.36385614405 / Phase error: 18.3641634542
RfactorNum. reflection% reflection
Rfree0.195095045293 2000 5.37894680222 %
Rwork0.157855371182 --
obs0.159897807 37182 94.1578667477 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 19.0193492644 Å2
Refinement stepCycle: LAST / Resolution: 1.8979→48.0201133545 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3938 0 101 321 4360
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006869930681164163
X-RAY DIFFRACTIONf_angle_d0.8599103396675642
X-RAY DIFFRACTIONf_chiral_restr0.0537102738096589
X-RAY DIFFRACTIONf_plane_restr0.00593814286363716
X-RAY DIFFRACTIONf_dihedral_angle_d19.74194809712444
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8979-1.94540.2531317813731440.1962542X-RAY DIFFRACTION96.4452423698
1.9454-1.9980.2453950300521450.1783241387622534X-RAY DIFFRACTION96.263025512
1.998-2.05680.2295008733581350.1729234937552383X-RAY DIFFRACTION91.0998552822
2.0568-2.12320.2066047901691460.1635643447732566X-RAY DIFFRACTION97.343862168
2.1232-2.19910.2115268255641450.1538797976852552X-RAY DIFFRACTION97.3997833153
2.1991-2.28710.2061654779351450.1590211113532551X-RAY DIFFRACTION96.7695620962
2.2871-2.39120.2245042107931450.1573452526382541X-RAY DIFFRACTION95.8600999286
2.3912-2.51730.224121887271350.1586354972532393X-RAY DIFFRACTION89.9644128114
2.5173-2.6750.2101806311571460.1603919555192557X-RAY DIFFRACTION96.2264150943
2.675-2.88150.2079259268151450.1614836854542553X-RAY DIFFRACTION95.8096590909
2.8815-3.17140.1629577038981410.1630141446942497X-RAY DIFFRACTION93.116837275
3.1714-3.63020.1938214277291420.1541773234742470X-RAY DIFFRACTION91.7779339424
3.6302-4.57310.1415429254141440.1304879434272531X-RAY DIFFRACTION92.8497049636
4.5731-48.020.178530742781420.1638962731742512X-RAY DIFFRACTION87.9973474801
Refinement TLS params.Method: refined / Origin x: -7.5640173885 Å / Origin y: 13.8603399316 Å / Origin z: -28.8504758483 Å
111213212223313233
T0.0472301935202 Å2-0.00961149589459 Å20.00226275136716 Å2-0.0515185882438 Å2-0.00111027709825 Å2--0.0524562176101 Å2
L0.0312367692087 °20.0406613160762 °2-0.0141164458728 °2-0.163346141644 °2-0.0450359136201 °2--0.0771501649191 °2
S0.010011332444 Å °0.0234214253908 Å °0.016148504402 Å °0.0486342286662 Å °-0.0255714695484 Å °0.00610892685711 Å °0.0248502172057 Å °0.00708529930936 Å °1.20054357005E-11 Å °
Refinement TLS groupSelection details: all

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