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- PDB-6kx5: Crystal structure of mouse Cryptochrome 1 in complex with KL044 c... -

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Basic information

Entry
Database: PDB / ID: 6kx5
TitleCrystal structure of mouse Cryptochrome 1 in complex with KL044 compound
ComponentsCryptochrome-1
KeywordsCIRCADIAN CLOCK PROTEIN / Cryptochrome / CRY / CRY1
Function / homology
Function and homology information


negative regulation of glucocorticoid secretion / negative regulation of glucocorticoid receptor signaling pathway / negative regulation of circadian rhythm / lipid storage / regulation of DNA damage checkpoint / response to glucagon / negative regulation of G protein-coupled receptor signaling pathway / regulation of gluconeogenesis / entrainment of circadian clock by photoperiod / E-box binding ...negative regulation of glucocorticoid secretion / negative regulation of glucocorticoid receptor signaling pathway / negative regulation of circadian rhythm / lipid storage / regulation of DNA damage checkpoint / response to glucagon / negative regulation of G protein-coupled receptor signaling pathway / regulation of gluconeogenesis / entrainment of circadian clock by photoperiod / E-box binding / photoreceptor activity / response to light stimulus / signal transduction in response to DNA damage / phosphatase binding / negative regulation of gluconeogenesis / positive regulation of gluconeogenesis / negative regulation of protein ubiquitination / FAD binding / positive regulation of protein ubiquitination / response to activity / gluconeogenesis / nuclear receptor binding / circadian regulation of gene expression / response to insulin / regulation of circadian rhythm / kinase binding / histone deacetylase binding / circadian rhythm / 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
Chem-DYR / Cryptochrome-1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMiller, S.A. / Aikawa, Y. / Hirota, T.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Science and TechnologyJPMJPR14LA Japan
Japan Society for the Promotion of Science15H05590 Japan
Japan Society for the Promotion of Science18H02402 Japan
CitationJournal: Nat.Chem.Biol. / Year: 2020
Title: Isoform-selective regulation of mammalian cryptochromes.
Authors: Miller, S. / Son, Y.L. / Aikawa, Y. / Makino, E. / Nagai, Y. / Srivastava, A. / Oshima, T. / Sugiyama, A. / Hara, A. / Abe, K. / Hirata, K. / Oishi, S. / Hagihara, S. / Sato, A. / Tama, F. / ...Authors: Miller, S. / Son, Y.L. / Aikawa, Y. / Makino, E. / Nagai, Y. / Srivastava, A. / Oshima, T. / Sugiyama, A. / Hara, A. / Abe, K. / Hirata, K. / Oishi, S. / Hagihara, S. / Sato, A. / Tama, F. / Itami, K. / Kay, S.A. / Hatori, M. / Hirota, T.
History
DepositionSep 10, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 1, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 15, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jun 3, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cryptochrome-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,7322
Polymers57,3721
Non-polymers3601
Water4,143230
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Monomeric in solution
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area21020 Å2
Unit cell
Length a, b, c (Å)44.410, 54.400, 61.420
Angle α, β, γ (deg.)63.900, 88.990, 83.650
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein Cryptochrome-1


Mass: 57371.734 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: Chemical ChemComp-DYR / 2-carbazol-9-yl-N-(2-chloranyl-6-cyano-phenyl)ethanamide


Mass: 359.808 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H14ClN3O / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 230 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.31 Å3/Da / Density % sol: 46.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 20% w/v PEG 3350, 3% v/v ethylene glycol, 200 mM NH4Cl
PH range: 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: Bruker DIP-6040 / Detector: CCD / Date: Jun 4, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2→35.04 Å / Num. obs: 34078 / % possible obs: 98.3 % / Redundancy: 4 % / CC1/2: 0.93 / Rpim(I) all: 0.134 / Rrim(I) all: 0.266 / Net I/σ(I): 4.6
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.518 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 4936 / CC1/2: 0.66

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Processing

Software
NameVersionClassification
PHENIX1refinement
REFMAC5refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6KX4

6kx4


Resolution: 2→35.04 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2303 1821 5.34 %
Rwork0.1765 --
obs0.1793 34078 98.31 %
Displacement parametersBiso mean: 22.12 Å2
Refinement stepCycle: LAST / Resolution: 2→35.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3731 0 26 230 3987
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00773866
X-RAY DIFFRACTIONf_angle_d0.86795266
X-RAY DIFFRACTIONf_chiral_restr0.0506563
X-RAY DIFFRACTIONf_plane_restr0.0062673
X-RAY DIFFRACTIONf_dihedral_angle_d17.22052255
LS refinement shellResolution: 2→2.1145 Å
RfactorNum. reflection% reflection
Rfree0.3225 167 -
Rwork0.2704 2459 -
obs--98 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0278-0.0058-0.01060.0378-0.00850.03630.00750.00090.0532-0.01410.03820.0067-0.06190.01220.00270.0993-0.00760.01760.04-0.02210.08262.1474-0.70148.8153
20.16190.0176-0.00440.05440.00210.0409-0.022-0.1493-0.18670.00670.00340.0236-0.00530.0139-0.0320.0216-0.0001-0.01660.0250.00570.01975.4852-25.340723.6719
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 230 )A2 - 230
2X-RAY DIFFRACTION2chain 'A' and (resid 231 through 490 )A231 - 490

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