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- PDB-6fn2: X-ray structure of animal-like Cryptochrome from Chlamydomonas re... -

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Basic information

Entry
Database: PDB / ID: 6fn2
TitleX-ray structure of animal-like Cryptochrome from Chlamydomonas reinhardtii
ComponentsCryptochrome photoreceptor
KeywordsFLAVOPROTEIN / Cryptochrome / Photolyase / Photoreceptor
Function / homology
Function and homology information


deoxyribodipyrimidine photo-lyase activity / entrainment of circadian clock by photoperiod / FAD binding / circadian regulation of gene expression / DNA binding / nucleus / cytoplasm
Similarity search - Function
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 / Chem-HDF / PHOSPHATE ION / Uncharacterized protein
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 Å
AuthorsFranz, S. / Ignatz, E. / Wenzel, S. / Zielosko, H. / Yamamoto, J. / Mittag, M. / Essen, L.-O.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationFOR 1261-2 Germany
CitationJournal: Nucleic Acids Res. / Year: 2018
Title: Structure of the bifunctional cryptochrome aCRY from Chlamydomonas reinhardtii.
Authors: Franz, S. / Ignatz, E. / Wenzel, S. / Zielosko, H. / Putu, E.P.G.N. / Maestre-Reyna, M. / Tsai, M.D. / Yamamoto, J. / Mittag, M. / Essen, L.O.
History
DepositionFeb 2, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 1, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 19, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cryptochrome photoreceptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,3638
Polymers57,8071
Non-polymers1,5567
Water4,648258
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3050 Å2
ΔGint-18 kcal/mol
Surface area19660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)150.249, 50.528, 64.970
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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 photoreceptor


Mass: 57807.066 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: UVR3, CHLREDRAFT_206002 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A8J8W0

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Non-polymers , 6 types, 265 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-HDF / 8-HYDROXY-10-(D-RIBO-2,3,4,5-TETRAHYDROXYPENTYL)-5-DEAZAISOALLOXAZINE


Mass: 363.322 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H17N3O7
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 258 / 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: 2.13 Å3/Da / Density % sol: 42.34 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.1 M MES, pH 6.0 with 15 % PEG 5000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.992 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.992 Å / Relative weight: 1
ReflectionResolution: 2.3→29.8 Å / Num. obs: 22003 / % possible obs: 96.6 % / Redundancy: 1.53 % / Biso Wilson estimate: 19.75 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 7.15
Reflection shellResolution: 2.3→2.4 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0123refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementResolution: 2.3→29.8 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.9 / SU B: 7.14 / SU ML: 0.175 / Cross valid method: THROUGHOUT / ESU R: 0.407 / ESU R Free: 0.241 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22753 682 3.1 %RANDOM
Rwork0.16778 ---
obs0.16963 21265 96.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 21.548 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å2-0 Å20 Å2
2--0.03 Å2-0 Å2
3---0.03 Å2
Refinement stepCycle: 1 / Resolution: 2.3→29.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3940 0 103 258 4301
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0194176
X-RAY DIFFRACTIONr_bond_other_d0.0020.023857
X-RAY DIFFRACTIONr_angle_refined_deg1.4371.9725702
X-RAY DIFFRACTIONr_angle_other_deg0.97838867
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4085490
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.0322.368190
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.80815624
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1231535
X-RAY DIFFRACTIONr_chiral_restr0.0870.2594
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214637
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021012
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2432.3711963
X-RAY DIFFRACTIONr_mcbond_other1.2422.3691962
X-RAY DIFFRACTIONr_mcangle_it2.0213.4242452
X-RAY DIFFRACTIONr_mcangle_other2.0213.4262453
X-RAY DIFFRACTIONr_scbond_it1.7112.5522213
X-RAY DIFFRACTIONr_scbond_other1.7092.5492209
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.7873.5823245
X-RAY DIFFRACTIONr_long_range_B_refined4.3199.6425117
X-RAY DIFFRACTIONr_long_range_B_other4.3199.6445118
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 46 -
Rwork0.19 1529 -
obs--97.04 %

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