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- PDB-4k0r: Crystal structure of mouse Cryptochrome 1 -

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Basic information

Entry
Database: PDB / ID: 4k0r
TitleCrystal structure of mouse Cryptochrome 1
ComponentsCryptochrome-1
KeywordsCIRCADIAN CLOCK PROTEIN / Rossmann fold / phosphorylation
Function / homology
Function and homology information


negative regulation of glucocorticoid secretion / negative regulation of glucocorticoid receptor signaling pathway / : / negative regulation of circadian rhythm / negative regulation of G protein-coupled receptor signaling pathway / lipid storage / regulation of DNA damage checkpoint / response to glucagon / regulation of gluconeogenesis / entrainment of circadian clock by photoperiod ...negative regulation of glucocorticoid secretion / negative regulation of glucocorticoid receptor signaling pathway / : / negative regulation of circadian rhythm / negative regulation of G protein-coupled receptor signaling pathway / lipid storage / regulation of DNA damage checkpoint / response to glucagon / regulation of gluconeogenesis / entrainment of circadian clock by photoperiod / E-box binding / photoreceptor activity / response to light stimulus / phosphatase binding / negative regulation of gluconeogenesis / signal transduction in response to DNA damage / positive regulation of gluconeogenesis / negative regulation of protein ubiquitination / FAD binding / response to activity / positive regulation of protein ubiquitination / gluconeogenesis / nuclear receptor binding / circadian regulation of gene expression / response to insulin / regulation of circadian rhythm / kinase binding / circadian rhythm / histone deacetylase binding / glucose homeostasis / double-stranded DNA binding / DNA-binding transcription factor binding / negative regulation of DNA-templated transcription / protein kinase binding / negative regulation of transcription by RNA polymerase II / mitochondrion / DNA binding / nucleoplasm / nucleus / cytosol / 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
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsCzarna, A. / Wolf, E.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2013
Title: Structures of Drosophila cryptochrome and mouse cryptochrome1 provide insight into circadian function.
Authors: Czarna, A. / Berndt, A. / Singh, H.R. / Grudziecki, A. / Ladurner, A.G. / Timinszky, G. / Kramer, A. / Wolf, E.
History
DepositionApr 4, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2013Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cryptochrome-1


Theoretical massNumber of molelcules
Total (without water)69,3671
Polymers69,3671
Non-polymers00
Water1,27971
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.170, 79.550, 127.390
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Cryptochrome-1 /


Mass: 69366.734 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cry1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P97784
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 71 / 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

Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2 M NH4Cl, 20% PEG 3350 , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 25, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.65→42 Å / Num. all: 13649 / Num. obs: 13625 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.65→2.7 Å / % possible all: 100

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Processing

Software
NameVersionClassification
XDSdata scaling
MOLREPphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.65→41.733 Å / SU ML: 0.37 / σ(F): 2.01 / Phase error: 22.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2598 682 5.01 %random
Rwork0.1901 ---
obs0.1936 13623 99.83 %-
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.56 Å2 / ksol: 0.372 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.6821 Å20 Å20 Å2
2---0.0002 Å2-0 Å2
3---1.6823 Å2
Refinement stepCycle: LAST / Resolution: 2.65→41.733 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3622 0 0 71 3693
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093722
X-RAY DIFFRACTIONf_angle_d1.2415068
X-RAY DIFFRACTIONf_dihedral_angle_d15.9151331
X-RAY DIFFRACTIONf_chiral_restr0.081550
X-RAY DIFFRACTIONf_plane_restr0.005652
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.65-2.85460.33771330.2342530X-RAY DIFFRACTION100
2.8546-3.14180.29741350.20912552X-RAY DIFFRACTION100
3.1418-3.59620.26231340.19392547X-RAY DIFFRACTION100
3.5962-4.52990.24471360.16512595X-RAY DIFFRACTION100
4.5299-41.73770.23661440.1912717X-RAY DIFFRACTION100

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