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

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Basic information

Entry
Database: PDB / ID: 9hnm
TitleStructure of the (6-4) photolyase of Caulobacter crescentus in its dark adapted and oxidized state determined by serial femtosecond crystallography
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 / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 1.71 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
Water4,936274
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1610 Å2
ΔGint-29 kcal/mol
Surface area20800 Å2
Unit cell
Length a, b, c (Å)49.800, 103.400, 104.800
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.: 274 / 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: 2.32 Å3/Da / Density % sol: 47.01 %
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: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SACLA / Beamline: BL2 / Wavelength: 1.24 Å
DetectorType: MPCCD / Detector: CCD / Date: Nov 4, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.24 Å / Relative weight: 1
ReflectionResolution: 1.71→24.23 Å / Num. obs: 59370 / % possible obs: 100 % / Redundancy: 1188 % / Biso Wilson estimate: 26.85 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.069 / Net I/σ(I): 11.38
Reflection shellResolution: 1.71→1.77 Å / Rmerge(I) obs: 1.134 / Mean I/σ(I) obs: 1.49 / Num. unique obs: 5836 / CC1/2: 0.5
Serial crystallography sample deliveryDescription: LCP extruder / Method: injection
Serial crystallography sample delivery injectionCarrier solvent: grease / Description: LCP extruder / Power by: HPLC
Preparation: Crystals transferred to carrier solvent under safety light
Serial crystallography data reductionCrystal hits: 74470 / Frames indexed: 59370

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.71→24.23 Å / SU ML: 0.1479 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.482
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1874 2891 4.88 %
Rwork0.1586 56387 -
obs0.16 59278 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.67 Å2
Refinement stepCycle: LAST / Resolution: 1.71→24.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4078 0 84 274 4436
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01674378
X-RAY DIFFRACTIONf_angle_d1.45385962
X-RAY DIFFRACTIONf_chiral_restr0.093607
X-RAY DIFFRACTIONf_plane_restr0.0164780
X-RAY DIFFRACTIONf_dihedral_angle_d8.9689602
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.71-1.740.25431240.25352640X-RAY DIFFRACTION100
1.74-1.770.26211330.24952668X-RAY DIFFRACTION100
1.77-1.80.261290.23492651X-RAY DIFFRACTION100
1.8-1.830.2441310.22712649X-RAY DIFFRACTION100
1.83-1.870.27111460.21862651X-RAY DIFFRACTION100
1.87-1.910.23211380.20752671X-RAY DIFFRACTION100
1.91-1.960.24791360.19842616X-RAY DIFFRACTION100
1.96-2.010.23821390.18882650X-RAY DIFFRACTION100
2.01-2.060.18611400.18452668X-RAY DIFFRACTION100
2.06-2.120.23111370.17852659X-RAY DIFFRACTION100
2.12-2.190.21941530.17322669X-RAY DIFFRACTION100
2.19-2.270.21721270.17062667X-RAY DIFFRACTION100
2.27-2.360.18491280.17262685X-RAY DIFFRACTION100
2.36-2.470.19881620.16782659X-RAY DIFFRACTION100
2.47-2.60.23991340.16862680X-RAY DIFFRACTION100
2.6-2.760.19171430.17142703X-RAY DIFFRACTION100
2.76-2.970.2071470.16982670X-RAY DIFFRACTION100
2.97-3.270.17141330.16382731X-RAY DIFFRACTION100
3.27-3.740.17551220.13972746X-RAY DIFFRACTION100
3.74-4.710.14051380.1182766X-RAY DIFFRACTION100
4.71-24.230.15321510.13572888X-RAY DIFFRACTION99.84
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)
12.197377938290.710582410202-0.5337072940144.15346434244-0.4214779532983.89287918676-0.1725891980280.672987243031-0.0719648774717-0.7132404801920.148133649855-0.2375891248020.2313762566340.2827136857330.011048482390.400275885066-0.03378291686230.004343281399030.492835124192-0.005304896112660.2419048476540.23476823341313.6486332453-11.3031996034
21.28092549072-0.212548053044-0.2353685839381.540775251780.4714546718571.21050549678-0.0363340763725-0.1767774401780.06800871092750.2323188238360.0498274091786-0.143820843189-0.03536505638890.190967988235-0.01857726472470.218484407322-0.0203773070849-0.02137464104270.2117577159380.02456339516770.18769183238310.321249017614.948281867432.7300265649
30.714879330881-0.787994495149-0.04362756028441.221946455310.2073790893570.9968348424320.03150799652120.179603178341-0.182124766899-0.0553862439745-0.1737688340010.16231126030.195367424856-0.1234104347680.1290853886640.313515867842-0.04790167528760.05517609834630.310866532291-0.0009662736791620.414410001784-1.51978509737-7.5175387884114.4949025299
40.790381700122-0.07798483398790.1624525291411.12547510356-0.3382583052760.943923205345-0.02691768281920.0834823924266-0.00541474184998-0.04738156770650.01225421126730.05548332189340.0198384358953-0.03021322869120.0174228773040.189752714799-0.01072205262690.006111595493250.2176548922340.008829772926960.218593907825-1.567362482338.308936463414.9414116031
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 440 through 508 )440 - 508440 - 508
22chain 'A' and (resid 1 through 161 )1 - 1611 - 161
33chain 'A' and (resid 162 through 200 )162 - 200162 - 200
44chain 'A' and (resid 201 through 439 )201 - 439201 - 439

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