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

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Basic information

Entry
Database: PDB / ID: 9hnk
TitleStructure of the (6-4) photolyase of Caulobacter crescentus in its oxidizd state - Singal crystal / 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: 1.59 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
Water8,935496
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1600 Å2
ΔGint-27 kcal/mol
Surface area20540 Å2
Unit cell
Length a, b, c (Å)49.274, 102.730, 103.893
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.: 496 / 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: 45.69 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 1.0M LiCl 0.1M MES (pH 6.0) 20% (w/v) PEG6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 10, 2022
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.59→46.36 Å / Num. obs: 737710 / % possible obs: 99.5 % / Redundancy: 10.2 % / Biso Wilson estimate: 21.44 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.114 / Net I/σ(I): 8.3
Reflection shellResolution: 1.59→1.65 Å / Rmerge(I) obs: 1.749 / Mean I/σ(I) obs: 1.41 / Num. unique obs: 7104 / CC1/2: 0.52

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.59→46.36 Å / SU ML: 0.1784 / Cross valid method: FREE R-VALUE / σ(F): 1.9 / Phase error: 22.1789
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2016 7047 5.14 %
Rwork0.181 130017 -
obs0.1821 137064 99.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.17 Å2
Refinement stepCycle: LAST / Resolution: 1.59→46.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4078 0 84 496 4658
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01554355
X-RAY DIFFRACTIONf_angle_d1.23185923
X-RAY DIFFRACTIONf_chiral_restr0.0741603
X-RAY DIFFRACTIONf_plane_restr0.024771
X-RAY DIFFRACTIONf_dihedral_angle_d9.5986596
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.59-1.60.30382090.29464227X-RAY DIFFRACTION96.06
1.6-1.620.28512380.28094333X-RAY DIFFRACTION99.98
1.62-1.640.2992170.27094436X-RAY DIFFRACTION99.94
1.64-1.660.29912080.2674331X-RAY DIFFRACTION99.93
1.66-1.680.30341740.26124421X-RAY DIFFRACTION99.96
1.68-1.710.2922310.24364412X-RAY DIFFRACTION99.94
1.71-1.730.24882280.23484390X-RAY DIFFRACTION99.89
1.73-1.760.25182280.22514374X-RAY DIFFRACTION99.87
1.76-1.790.27252520.21594303X-RAY DIFFRACTION99.89
1.79-1.810.2492770.21934346X-RAY DIFFRACTION99.94
1.81-1.850.24622320.22044327X-RAY DIFFRACTION99.5
1.85-1.880.22522340.22064390X-RAY DIFFRACTION99.81
1.88-1.920.25352220.26124150X-RAY DIFFRACTION94.57
1.92-1.950.27312070.24844202X-RAY DIFFRACTION95.66
1.95-20.21342060.19774387X-RAY DIFFRACTION99.85
2-2.040.22142870.18964351X-RAY DIFFRACTION99.91
2.04-2.090.20162440.18694325X-RAY DIFFRACTION99.93
2.09-2.150.19052540.18264388X-RAY DIFFRACTION99.89
2.15-2.210.20522110.18074356X-RAY DIFFRACTION99.93
2.21-2.290.25651960.22424054X-RAY DIFFRACTION92.31
2.29-2.370.17432930.17474339X-RAY DIFFRACTION100
2.37-2.460.21293000.1674292X-RAY DIFFRACTION99.93
2.46-2.570.18882530.17284355X-RAY DIFFRACTION99.81
2.57-2.710.18132380.1724365X-RAY DIFFRACTION99.83
2.71-2.880.18752050.16734414X-RAY DIFFRACTION99.96
2.88-3.10.1982030.17034408X-RAY DIFFRACTION99.93
3.1-3.410.18812050.1644367X-RAY DIFFRACTION99.96
3.41-3.910.18252820.154306X-RAY DIFFRACTION99.59
3.91-4.920.13852550.13834340X-RAY DIFFRACTION99.2
4.92-46.360.21362580.1744328X-RAY DIFFRACTION99.63
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)
10.743246733854-0.1559418134410.2296979010451.32869840445-0.3936551577630.929769980586-0.01331462655530.0659540832316-0.0460223596681-0.03981506140190.0004065859587630.01584332030.0460627253057-0.006460591486150.01746818620.120314859129-0.00217695738770.007023649936080.1279995927680.002803040759930.140753189750.676141913467.2763660648113.6685686418
21.955944148170.7703180635170.005582248087883.09840832244-0.1422749265772.54391432913-0.02936229911090.426689310622-0.170486130487-0.601495542052-0.018190160082-0.2151561684730.3295280157080.3047599391750.03218427412710.2998671668620.05874928804540.0246321962440.31908835728-0.003313359439430.190560072983-1.1261330958111.9883117617-9.72774012851
30.917007961988-0.139498338465-0.2295084504141.254517035180.5551311073521.20428743337-0.0252224992958-0.0134086357369-0.0003187011175170.09374449070850.0279101749408-0.024763476156-0.01970490519940.0419459166034-0.0005079373782840.149193671964-0.000584287269484-9.48598460607E-50.1271482660540.04163733513740.1286378362985.5152052929711.73265525528.7912257866
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 230 through 426 )230 - 426230 - 426
22chain 'A' and (resid 427 through 508 )427 - 508427 - 508
33chain 'A' and (resid 1 through 229 )1 - 2291 - 229

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