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- PDB-7ud0: Room Temperature Drosophila Cryptochrome -

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Basic information

Entry
Database: PDB / ID: 7ud0
TitleRoom Temperature Drosophila Cryptochrome
ComponentsCryptochrome-1
KeywordsCIRCADIAN CLOCK PROTEIN / light-sensor
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 / regulation of circadian sleep/wake cycle, sleep ...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 / regulation of circadian sleep/wake cycle, sleep / cellular response to light stimulus / blue light photoreceptor activity / response to blue light / entrainment of circadian clock / circadian behavior / entrainment of circadian clock by photoperiod / locomotor rhythm / response to light stimulus / photoreceptor activity / phototransduction / FAD binding / circadian regulation of gene expression / circadian rhythm / regulation of circadian rhythm / flavin adenine dinucleotide binding / negative regulation of DNA-templated transcription / perinuclear region of cytoplasm / DNA binding / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
DNA Cyclobutane Dipyrimidine Photolyase, subunit A; domain 3 / DNA Cyclobutane Dipyrimidine Photolyase, subunit A, domain 3 / 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 ...DNA Cyclobutane Dipyrimidine Photolyase, subunit A; domain 3 / DNA Cyclobutane Dipyrimidine Photolyase, subunit A, domain 3 / 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 / Rossmann-like alpha/beta/alpha sandwich fold / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Cryptochrome-1
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsSchneps, C.M. / Crane, B.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)R35122535 United States
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2022
Title: Room-temperature serial synchrotron crystallography of Drosophila cryptochrome.
Authors: Schneps, C.M. / Ganguly, A. / Crane, B.R.
History
DepositionMar 17, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)126,1474
Polymers124,5762
Non-polymers1,5712
Water00
1
A: Cryptochrome-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,0742
Polymers62,2881
Non-polymers7861
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cryptochrome-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,0742
Polymers62,2881
Non-polymers7861
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.000, 123.000, 81.000
Angle α, β, γ (deg.)90.000, 116.000, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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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: cry, CG3772 / Plasmid: pET28a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): CmpX13 / References: UniProt: O77059
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
Has ligand of interestY
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: 2.66 Å3/Da / Density % sol: 53.75 %
Crystal growTemperature: 298 K / Method: batch mode / pH: 8.5
Details: 5 mg/mL twin-strep tagged dCRY (1-539) 100 mM Tris (pH 8.5) 150 mM Magnesium acetate tetrahydrate 18% PEG-4000 Mixed 1:1 in Eppendorf tube; no vortexing

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Data collection

DiffractionMean temperature: 298 K / Ambient temp details: Room Temperature / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 1.1271 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Apr 12, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1271 Å / Relative weight: 1
ReflectionResolution: 3.5→19.84 Å / Num. obs: 14881 / % possible obs: 89.8 % / Redundancy: 47.4 % / Biso Wilson estimate: 100.7 Å2 / CC1/2: 0.269 / Rmerge(I) obs: 0.649 / Rrim(I) all: 0.658 / Net I/σ(I): 5.9
Reflection shellResolution: 3.5→3.63 Å / Redundancy: 48.6 % / Rmerge(I) obs: 2.52 / Mean I/σ(I) obs: 2 / Num. unique obs: 1462 / CC1/2: 0.213 / Rrim(I) all: 2.55 / % possible all: 89.1
Serial crystallography sample deliveryMethod: fixed target
Serial crystallography sample delivery fixed targetDescription: Batch crystallization
Sample dehydration prevention: Sealed chips with mylar films
Sample holding: chip
Sample solvent: 100 mM Tris (pH 8.5), 150 mM Magnesium acetate tetrahydrate, 18% PEG-4000
Sample unit size: 10 µm / Support base: goniometer

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX1.17.1refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GU5

4gu5


Resolution: 3.5→19.84 Å / Cross valid method: FREE R-VALUE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.294 -10 %1419
Rwork0.251 ---
obs-14126 89.8 %-
Displacement parametersBiso mean: 99.65 Å2
Refinement stepCycle: LAST / Resolution: 3.5→19.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8747 0 106 0 8853
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00429103
X-RAY DIFFRACTIONf_angle_d0.585812390
X-RAY DIFFRACTIONf_chiral_restr0.03931311
X-RAY DIFFRACTIONf_plane_restr0.00311600
X-RAY DIFFRACTIONf_dihedral_angle_d18.78823322
LS refinement shellResolution: 3.5→3.63 Å
RfactorNum. reflection% reflection
Rfree0.329 --
Rwork0.296 1221 -
obs--89.1 %

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