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- PDB-9hnl: Structure of the (6-4) photolyase of Caulobacter crescentus in it... -

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Basic information

Entry
Database: PDB / ID: 9hnl
TitleStructure of the (6-4) photolyase of Caulobacter crescentus in its oxidized state at room temperture-synchrotron
ComponentsCryptochrome/photolyase family protein
KeywordsFLAVOPROTEIN / DNA repair / photolyase / electron transfer / iron-sulfur cluster
Function / homologyPhotolyase PhrB-like / : / Deoxyribodipyrimidine photo-lyase-related protein / Cryptochrome/DNA photolyase, FAD-binding domain-like superfamily / Rossmann-like alpha/beta/alpha sandwich fold / Chem-DLZ / FLAVIN-ADENINE DINUCLEOTIDE / IRON/SULFUR CLUSTER / Cryptochrome/photolyase family protein
Function and homology information
Biological speciesCaulobacter vibrioides (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsPo Hsun, W. / Maestre-Reyna, M. / Essen, L.-O.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)ES152/18 Germany
CitationJournal: J.Am.Chem.Soc. / Year: 2025
Title: Redox-State-Dependent Structural Changes within a Prokaryotic 6-4 Photolyase.
Authors: Wang, P.H. / Hosokawa, Y. / C Soares, J. / Emmerich, H.J. / Fuchs, V. / Caramello, N. / Engilberge, S. / Bologna, A. / Rosner, C.J. / Nakamura, M. / Watad, M. / Luo, F. / Owada, S. / Tosha, ...Authors: Wang, P.H. / Hosokawa, Y. / C Soares, J. / Emmerich, H.J. / Fuchs, V. / Caramello, N. / Engilberge, S. / Bologna, A. / Rosner, C.J. / Nakamura, M. / Watad, M. / Luo, F. / Owada, S. / Tosha, T. / Kang, J. / Tono, K. / Bessho, Y. / Nango, E. / Pierik, A.J. / Royant, A. / Tsai, M.D. / Yamamoto, J. / Maestre-Reyna, M. / Essen, L.O.
History
DepositionDec 11, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 7, 2025Provider: repository / Type: Initial release
Revision 1.1May 21, 2025Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cryptochrome/photolyase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,5854
Polymers58,1211
Non-polymers1,4633
Water5,801322
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1590 Å2
ΔGint-28 kcal/mol
Surface area20510 Å2
Unit cell
Length a, b, c (Å)49.347, 102.677, 103.539
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/photolyase family protein


Mass: 58121.285 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caulobacter vibrioides (bacteria) / Gene: CC_0646 / Production host: Escherichia coli B (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Gold / References: UniProt: Q9AAF5
#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-DLZ / 1-deoxy-1-(6,7-dimethyl-2,4-dioxo-3,4-dihydropteridin-8(2H)-yl)-D-ribitol / 6,7-dimethyl-8-(1'-D-ribityl) lumazine


Mass: 326.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H18N4O6 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 322 / 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: 2.26 Å3/Da / Density % sol: 45.49 %
Crystal growTemperature: 293 K / Method: batch mode / pH: 8.5 / Details: 0.1 M Tris (pH 8.5) 0.2 M MgCl2 20% (w/v) PEG3350

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Mar 26, 2020
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→45.99 Å / Num. obs: 27390 / % possible obs: 99.6 % / Redundancy: 4 % / Biso Wilson estimate: 26.75 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.2 / Net I/σ(I): 7.5
Reflection shellResolution: 2.2→2.28 Å / Rmerge(I) obs: 1.065 / Mean I/σ(I) obs: 1.89 / Num. unique obs: 2689 / CC1/2: 0.524

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→45.99 Å / SU ML: 0.236 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.0819
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2375 1322 4.84 %
Rwork0.1932 26013 -
obs0.1953 27335 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.31 Å2
Refinement stepCycle: LAST / Resolution: 2.2→45.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4078 0 84 322 4484
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00224295
X-RAY DIFFRACTIONf_angle_d0.52985835
X-RAY DIFFRACTIONf_chiral_restr0.038596
X-RAY DIFFRACTIONf_plane_restr0.0042756
X-RAY DIFFRACTIONf_dihedral_angle_d7.9774583
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.290.28511300.25842856X-RAY DIFFRACTION99.97
2.29-2.390.29181590.24672837X-RAY DIFFRACTION99.97
2.39-2.520.30011520.23272845X-RAY DIFFRACTION99.97
2.52-2.680.27171490.22762856X-RAY DIFFRACTION99.97
2.68-2.880.24581640.21952872X-RAY DIFFRACTION100
2.88-3.170.22791330.20212891X-RAY DIFFRACTION99.83
3.17-3.630.23051320.18022908X-RAY DIFFRACTION99.8
3.63-4.570.20831500.15112940X-RAY DIFFRACTION99.48
4.58-45.990.20871530.17163008X-RAY DIFFRACTION97.53
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)
11.10808468907-0.0730729286731-0.03522014193471.074808877520.5193207808621.12941082301-0.00633683994571-0.1078749582920.08664940027330.11895486870.0385226390326-0.124378988619-0.0235262399470.107534754156-0.0169797453770.23463243136-0.00925566804398-0.01172502142010.1936156516760.03018411880140.18199852823210.161375688514.849282855232.4237502428
21.88994153157-0.716356018784-0.07752676540541.298993883690.1739152618160.656189466755-0.0009359370260250.263609683546-0.300071659126-0.0929540940954-0.09019318147030.1790355566440.200456637519-0.07499584473010.1386849364310.284837877406-0.05901352651570.07632949531760.245544960799-0.01850034108730.323496060617-2.12549161189-7.0751778362414.3337958987
30.8641311721610.01433012821190.07351036610211.25302176347-0.408304033981.18127349867-0.04089033545570.193830646121-0.00401825456709-0.1592435840880.00132377176912-0.001323762209110.00776114699302-0.003867651470040.04381424000260.137498859864-0.0108273593476-0.01097242768830.175601609794-0.004054999943410.136757299911-1.154136518959.495709878988.66144915609
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 1 through 161 )1 - 1611 - 161
22chain 'A' and (resid 162 through 200 )162 - 200162 - 200
33chain 'A' and (resid 201 through 508 )201 - 508201 - 508

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