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- PDB-4k03: Crystal structure of Drosophila Cryprochrome -

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Basic information

Entry
Database: PDB / ID: 4k03
TitleCrystal structure of Drosophila Cryprochrome
ComponentsCryptochrome-1
KeywordsCIRCADIAN CLOCK PROTEIN / Rossmann fold / photoreceptor / FAD
Function / homology
Function and homology information


UV-A, blue light phototransduction / magnetoreception / detection of light stimulus involved in magnetoreception / gravitaxis / Phosphorylation of PER and TIM / Degradation of CRY / Degradation of TIM / blue light signaling pathway / response to magnetism / response to blue light ...UV-A, blue light phototransduction / magnetoreception / detection of light stimulus involved in magnetoreception / gravitaxis / Phosphorylation of PER and TIM / Degradation of CRY / Degradation of TIM / blue light signaling pathway / response to magnetism / response to blue light / regulation of circadian sleep/wake cycle, sleep / cellular response to light stimulus / blue light photoreceptor activity / entrainment of circadian clock / circadian behavior / entrainment of circadian clock by photoperiod / locomotor rhythm / photoreceptor activity / phototransduction / response to light stimulus / FAD binding / circadian regulation of gene expression / regulation of circadian rhythm / circadian rhythm / flavin adenine dinucleotide binding / negative regulation of DNA-templated transcription / perinuclear region of cytoplasm / 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
FLAVIN-ADENINE DINUCLEOTIDE / Cryptochrome-1
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsBerndt, 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 3, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cryptochrome-1
B: Cryptochrome-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,2904
Polymers128,7192
Non-polymers1,5712
Water93752
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3630 Å2
ΔGint-17 kcal/mol
Surface area43260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.120, 121.810, 79.720
Angle α, β, γ (deg.)90.00, 114.78, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Cryptochrome-1 / DmCRY1 / dcry / Blue light photoreceptor


Mass: 64359.441 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: cry, CG3772 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O77059
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 49.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 100 mM TrisHCl pH 8.0, 17% PEG 3350, 120 mM Mg-Acetate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9789 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 29, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 3.2→46 Å / Num. all: 20433 / Num. obs: 20372 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 3.2→3.37 Å / % possible all: 99.6

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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: 3.2→40.486 Å / SU ML: 0.44 / σ(F): 1.36 / Phase error: 27.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2687 1041 5.11 %random
Rwork0.1878 ---
obs0.1922 20357 99.68 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 55.825 Å2 / ksol: 0.346 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.2501 Å20 Å20.4499 Å2
2--1.1577 Å2-0 Å2
3---0.0924 Å2
Refinement stepCycle: LAST / Resolution: 3.2→40.486 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8588 0 106 52 8746
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0118943
X-RAY DIFFRACTIONf_angle_d1.51912192
X-RAY DIFFRACTIONf_dihedral_angle_d18.8873289
X-RAY DIFFRACTIONf_chiral_restr0.0931304
X-RAY DIFFRACTIONf_plane_restr0.0071654
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2001-3.36870.34011440.24082746X-RAY DIFFRACTION100
3.3687-3.57960.28441510.21812748X-RAY DIFFRACTION100
3.5796-3.85580.29771550.18582725X-RAY DIFFRACTION100
3.8558-4.24350.22991150.16432792X-RAY DIFFRACTION100
4.2435-4.85660.22811590.15562755X-RAY DIFFRACTION100
4.8566-6.11540.29421580.20032761X-RAY DIFFRACTION100
6.1154-40.48880.25531590.1852789X-RAY DIFFRACTION99

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