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- PDB-5zm0: X-ray structure of animal-like Cryptochrome from Chlamydomonas re... -

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Basic information

Entry
Database: PDB / ID: 5zm0
TitleX-ray structure of animal-like Cryptochrome from Chlamydomonas reinhardtii
ComponentsCryptochrome photoreceptor
KeywordsFLAVOPROTEIN / Cryptochrome / Photolyase / Photoreceptor
Function / homology
Function and homology information


deoxyribodipyrimidine photo-lyase activity / entrainment of circadian clock by photoperiod / FAD binding / circadian regulation of gene expression / DNA binding / nucleus / 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 / Uncharacterized protein
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsFranz, S. / Ignatz, E. / Wenzel, S. / Zielosko, H. / Gusti Ngurah Putu, E.P. / Maestre-Reyna, M. / Tsai, M.-D. / Yamamoto, J. / Mittag, M. / Essen, L.-O.
Funding support Germany, Taiwan, 2items
OrganizationGrant numberCountry
German Research FoundationFOR 1261-2 Germany
Ministry of Science and Technology (China)MOST107-0210-01-19-02 Taiwan
CitationJournal: Nucleic Acids Res. / Year: 2018
Title: Structure of the bifunctional cryptochrome aCRY from Chlamydomonas reinhardtii
Authors: Franz, S. / Ignatz, E. / Wenzel, S. / Zielosko, H. / Putu, E.P.G.N. / Maestre-Reyna, M. / Tsai, M.D. / Yamamoto, J. / Mittag, M. / Essen, L.O.
History
DepositionMar 31, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 25, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 26, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Nov 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 photoreceptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,59613
Polymers57,8071
Non-polymers1,78812
Water13,926773
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-11 kcal/mol
Surface area20220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.210, 65.120, 151.980
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Cryptochrome photoreceptor


Mass: 57807.066 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: UVR3, CHLRE_06g278251v5, CHLREDRAFT_206002 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A8J8W0

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Non-polymers , 5 types, 785 molecules

#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 773 / 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
IDDensity Matthews (Å3/Da)Density % sol (%)
42.1642.96
1
2
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: .1 M 2-(N-morpholino)ethanesulfonic acid (MES), pH 6.0, 35 % PEG 4000

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21002
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONBESSY 14.310.8944
SYNCHROTRONNSRRC TPS 05A20.99984
Detector
TypeIDDetectorDate
RAYONIX MX-2251CCDDec 19, 2013
RAYONIX MX300-HS2CCDMar 8, 2018
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.89441
20.999841
ReflectionResolution: 1.6→39.76 Å / Num. obs: 66645 / % possible obs: 100 % / Redundancy: 13.29 % / Biso Wilson estimate: 10.01 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.275 / Rrim(I) all: 0.286 / Net I/σ(I): 8.5
Reflection shellResolution: 1.6→1.657 Å / Redundancy: 10.16 % / Rmerge(I) obs: 1.68 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 6554 / CC1/2: 0.506 / Rrim(I) all: 1.777 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX.13-2998refinement
XDSJan 26, 2018data reduction
XSCALEJan 26, 2018data scaling
PHASER2.7.0phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CVV

3cvv


Resolution: 1.6→39.76 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflectionSelection details
Rfree0.1881 3302 5 %random selection
Rwork0.1526 ---
obs-66621 100 %-
Displacement parametersBiso mean: 15.17 Å2
Refinement stepCycle: LAST / Resolution: 1.6→39.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3874 0 113 774 4761

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