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- PDB-4gu5: Structure of Full-length Drosophila Cryptochrome -

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Basic information

Entry
Database: PDB / ID: 4gu5
TitleStructure of Full-length Drosophila Cryptochrome
ComponentsCryptochrome-1
KeywordsSIGNALING PROTEIN / PHOTOLYASE / CIRCADIAN CLOCK LIGHT ENTRAINMENT / GENE REGULATION / PROTEIN DEGRADATION / TIMELESS / JETLAG / PHOSPHORYLATION
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: 2.3 Å
AuthorsZoltowski, B.D. / Vaidya, A.T. / Top, D. / Widom, J. / Young, M.W. / Levy, C. / Jones, A.R. / Scrutton, N.S. / Leys, D. / Crane, B.R.
Citation
#1: Journal: Nature / Year: 2011
Title: Structure of full-length Drosophila cryptochrome.
Authors: Zoltowski, B.D. / Vaidya, A.T. / Top, D. / Widom, J. / Young, M.W. / Crane, B.R.
History
DepositionAug 29, 2012Deposition site: RCSB / Processing site: RCSB
SupersessionSep 26, 2012ID: 3TVS
Revision 1.0Sep 26, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2013Group: Database references
Revision 1.2Apr 3, 2013Group: Database references
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)126,1966
Polymers124,5762
Non-polymers1,6204
Water5,783321
1
A: Cryptochrome-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,0983
Polymers62,2881
Non-polymers8102
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cryptochrome-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,0983
Polymers62,2881
Non-polymers8102
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.750, 122.320, 75.030
Angle α, β, γ (deg.)90.00, 114.92, 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: 62288.051 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: CG3772, cry / Plasmid: PFASTBAC-HTA / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9 / References: UniProt: O77059
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


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


Mass: 18.015 Da / Num. of mol.: 321 / 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: 2.43 Å3/Da / Density % sol: 49.39 %
Crystal growTemperature: 298 K / pH: 8
Details: 50 MM HEPES PH 8.0; 150 MM NACL 5MG/ML PROTEIN MIXED 1:1 WITH 18% PDG 4K, 150 MM MGACETATE, 100 MM TRIS PH 8.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9793
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 12, 2008
RadiationMonochromator: 111 SI SIDE-BOUNCE MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.3→30.58 Å / Num. obs: 44381 / % possible obs: 84 % / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Rmerge(I) obs: 0.126 / Net I/σ(I): 11.9
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.354 / Mean I/σ(I) obs: 1.8 / % possible all: 48

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TEZ

1tez


Resolution: 2.3→30.58 Å / SU ML: 0.33 / σ(F): 0 / Phase error: 26.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.247 3585 8.08 %
Rwork0.184 --
obs0.189 44381 84 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 27.03 Å2 / ksol: 0.36 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-10.056 Å2-0 Å22.385 Å2
2---7.8556 Å2-0 Å2
3----2.2004 Å2
Refine analyzeLuzzati sigma a free: 0.33 Å
Refinement stepCycle: LAST / Resolution: 2.3→30.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8751 0 108 321 9180
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0089116
X-RAY DIFFRACTIONf_angle_d1.12712409
X-RAY DIFFRACTIONf_dihedral_angle_d19.3273423
X-RAY DIFFRACTIONf_chiral_restr0.0741311
X-RAY DIFFRACTIONf_plane_restr0.0051605
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3002-2.38240.3212030.2422298X-RAY DIFFRACTION48
2.3824-2.47770.30642490.2222929X-RAY DIFFRACTION60
2.4777-2.59040.30892750.22713480X-RAY DIFFRACTION71
2.5904-2.72690.29583750.21584062X-RAY DIFFRACTION85
2.7269-2.89760.28073810.21254334X-RAY DIFFRACTION89
2.8976-3.12120.27264180.19714542X-RAY DIFFRACTION94
3.1212-3.43490.25274200.17644670X-RAY DIFFRACTION97
3.4349-3.9310.21974700.15854736X-RAY DIFFRACTION98
3.931-4.94930.20374120.15114814X-RAY DIFFRACTION99
4.9493-30.58270.23033820.18774931X-RAY DIFFRACTION99

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