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- PDB-8z3d: SFX structure of CraCRY 1 us after photoexcitation of the oxidize... -

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Basic information

Entry
Database: PDB / ID: 8z3d
TitleSFX structure of CraCRY 1 us after photoexcitation of the oxidized protein
ComponentsCryptochrome photoreceptor
KeywordsFLAVOPROTEIN / photoreceptor / time-resolved crystallography / 1 us time-point
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
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
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Uncharacterized protein
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMaestre-Reyna, M. / Hosokawa, Y. / Wang, P.-H. / Saft, M. / Caramello, N. / Engilberge, S. / Franz-Badur, S. / Ngura Putu, E.P.G. / Nakamura, M. / Wu, W.-J. ...Maestre-Reyna, M. / Hosokawa, Y. / Wang, P.-H. / Saft, M. / Caramello, N. / Engilberge, S. / Franz-Badur, S. / Ngura Putu, E.P.G. / Nakamura, M. / Wu, W.-J. / Wu, H.-Y. / Lee, C.-C. / Huang, W.-C. / Huang, K.-F. / Chang, Y.-K. / Yang, C.-H. / Lin, W.-T. / Yang, K.-C. / Ban, Y. / Imura, T. / Kazuoka, A. / Tanida, E. / Owada, S. / Joti, Y. / Tanaka, R. / Tanaka, T. / Luo, F. / Tono, K. / Kiontke, S. / Korf, L. / Umena, Y. / Tosha, T. / Bessho, Y. / Nango, E. / Iwata, S. / Royant, A. / Tsai, M.-D. / Yamamoto, J. / Essen, L.-O.
Funding support Taiwan, Japan, 8items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, Taiwan)AS-KPQ-105-TPP Taiwan
Ministry of Science and Technology (MoST, Taiwan)AS-KPQ-109-TPP2 Taiwan
Ministry of Education, Culture, Sports, Science and Technology (Japan)JP20H05442 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)JP22H04751 Japan
Japan Science and TechnologyJPMJFR2057 Japan
Japan Society for the Promotion of Science (JSPS)JP19H05776 Japan
National Science Council (NSC, Taiwan)111-2113-M-002-029-MY3 Taiwan
Japan Society for the Promotion of Science (JSPS)JP21J13329 Japan
CitationJournal: Sci Adv / Year: 2025
Title: Capturing structural intermediates in an animal-like cryptochrome photoreceptor by time-resolved crystallography.
Authors: Maestre-Reyna, M. / Hosokawa, Y. / Wang, P.H. / Saft, M. / Caramello, N. / Engilberge, S. / Franz-Badur, S. / Gusti Ngurah Putu, E.P. / Nakamura, M. / Wu, W.J. / Wu, H.Y. / Lee, C.C. / ...Authors: Maestre-Reyna, M. / Hosokawa, Y. / Wang, P.H. / Saft, M. / Caramello, N. / Engilberge, S. / Franz-Badur, S. / Gusti Ngurah Putu, E.P. / Nakamura, M. / Wu, W.J. / Wu, H.Y. / Lee, C.C. / Huang, W.C. / Huang, K.F. / Chang, Y.K. / Yang, C.H. / Fong, M.I. / Lin, W.T. / Yang, K.C. / Ban, Y. / Imura, T. / Kazuoka, A. / Tanida, E. / Owada, S. / Joti, Y. / Tanaka, R. / Tanaka, T. / Kang, J. / Luo, F. / Tono, K. / Kiontke, S. / Korf, L. / Umena, Y. / Tosha, T. / Bessho, Y. / Nango, E. / Iwata, S. / Royant, A. / Tsai, M.D. / Yamamoto, J. / Essen, L.O.
History
DepositionApr 15, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 14, 2025Provider: repository / Type: Initial release
Revision 1.1May 28, 2025Group: 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

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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)58,6283
Polymers57,8071
Non-polymers8212
Water4,017223
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1380 Å2
ΔGint-17 kcal/mol
Surface area20510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.840, 65.600, 153.130
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#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
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 223 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.21 Å3/Da / Density % sol: 44.31 %
Crystal growTemperature: 277 K / Method: batch mode / pH: 5.6 / Details: 0.1 M MES, pH 5.6 (w/v) PEG 4000

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SACLA / Beamline: BL2 / Wavelength: 1.24 Å
DetectorType: MPCCD / Detector: CCD / Date: Apr 25, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.24 Å / Relative weight: 1
ReflectionResolution: 1.83→32.07 Å / Num. obs: 43294 / % possible obs: 99.95 % / Redundancy: 275 % / Biso Wilson estimate: 11.26 Å2 / CC1/2: 0.991 / Net I/σ(I): 6.76
Reflection shellResolution: 1.83→1.91 Å / Mean I/σ(I) obs: 1.42 / Num. unique obs: 2113 / CC1/2: 0.515
Serial crystallography measurementFocal spot size: 1.77 µm2 / Pulse duration: 10 fsec. / Pulse photon energy: 10 keV / XFEL pulse repetition rate: 30 Hz
Serial crystallography sample deliveryMethod: injection
Serial crystallography sample delivery injectionCarrier solvent: grease / Description: High viscosity injector / Filter size: 50 µm / Flow rate: 2.8 µL/min / Injector diameter: 75 µm / Injector temperature: 293 K

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
CrystFELdata reduction
pointlessdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6FN3

6fn3


Resolution: 2→30.58 Å / SU ML: 0.1853 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 22.2907
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2246 1105 3.12 %
Rwork0.1998 34352 -
obs0.2006 35457 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 13.09 Å2
Refinement stepCycle: LAST / Resolution: 2→30.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3910 0 54 223 4187
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034193
X-RAY DIFFRACTIONf_angle_d0.60265740
X-RAY DIFFRACTIONf_chiral_restr0.0401596
X-RAY DIFFRACTIONf_plane_restr0.0056743
X-RAY DIFFRACTIONf_dihedral_angle_d14.70781530
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.090.30851320.28244220X-RAY DIFFRACTION100
2.09-2.20.26111400.26284235X-RAY DIFFRACTION100
2.2-2.340.26971410.24544222X-RAY DIFFRACTION100
2.34-2.520.27011230.23844284X-RAY DIFFRACTION100
2.52-2.770.23951540.22784227X-RAY DIFFRACTION100
2.77-3.170.2361430.2114299X-RAY DIFFRACTION100
3.17-40.18131390.16434322X-RAY DIFFRACTION100
4-30.580.15111330.12364543X-RAY DIFFRACTION99.89
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)
10.5148943431410.0340455038284-0.1724960707120.7727714408250.148366539140.6959283687210.0174458281390.02602545659950.0533356879507-0.0137028005213-0.009257751492140.0150725700571-0.0531235351766-0.048219102624-0.02130790924450.04224837823340.00450697262014-0.01452367916150.05569417482250.007677299880640.043952306050719.6158931498.00091652408-15.6282094061
20.6495886740210.2081374435750.05343713334390.514336973610.0404583891120.3461202541760.001430879881380.0478461441794-0.044134427859-0.04118870632480.01004327570040.02903206100220.0258891698488-0.0222864780469-0.01218851182120.04189117226310.007948844357490.002983717304770.0426851678557-0.003428244447410.031117662443712.1400220471-18.0669217975-24.99595121
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 3 through 214 )3 - 2141 - 209
22chain 'A' and (resid 215 through 494 )215 - 494210 - 489

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