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

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Basic information

Entry
Database: PDB / ID: 9hno
TitleStructure of the (6-4) photolyase of Caulobacter crescentus in its iron sulfur cluster 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: 2.3 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

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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
Water4,702261
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1630 Å2
ΔGint-29 kcal/mol
Surface area20810 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.: 261 / 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: 2.3→24.9 Å / Num. obs: 47810 / % possible obs: 100 % / Redundancy: 1090 % / Biso Wilson estimate: 25.15 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.08 / Net I/σ(I): 10.55
Reflection shellResolution: 2.3→2.38 Å / Rmerge(I) obs: 1.095 / Mean I/σ(I) obs: 1.49 / Num. unique obs: 2436 / CC1/2: 0.524
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: 84237 / Frames indexed: 59143

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→24.9 Å / SU ML: 0.3063 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 30.5973
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2644 1221 4.94 %
Rwork0.2171 23512 -
obs0.2195 24733 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.48 Å2
Refinement stepCycle: LAST / Resolution: 2.3→24.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4056 0 84 261 4401
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024313
X-RAY DIFFRACTIONf_angle_d0.48245868
X-RAY DIFFRACTIONf_chiral_restr0.0352601
X-RAY DIFFRACTIONf_plane_restr0.0035761
X-RAY DIFFRACTIONf_dihedral_angle_d8.2914592
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.390.35711470.34882567X-RAY DIFFRACTION100
2.39-2.50.40381490.34392556X-RAY DIFFRACTION100
2.5-2.630.42441300.33152572X-RAY DIFFRACTION100
2.63-2.80.35531400.31022555X-RAY DIFFRACTION100
2.8-3.010.35731250.27982591X-RAY DIFFRACTION100
3.01-3.320.31291400.2432616X-RAY DIFFRACTION100
3.32-3.790.19671120.18762639X-RAY DIFFRACTION100
3.79-4.770.17021350.14832648X-RAY DIFFRACTION100
4.77-24.90.18971430.1342768X-RAY DIFFRACTION99.73
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)
10.6603154548520.421680339628-0.4868347115611.507868347430.1607185480221.02422808225-0.07607066278680.2772013871230.0508437305475-0.204114674028-0.01948426177450.2219894331650.0703946118778-0.09852497270490.03139345262010.1624385632480.00754064871023-0.02228816102930.213170125459-0.01310331346870.170498105385-0.87411474469511.50706473823.72717884158
20.315077691238-0.265984838849-0.619188891140.2966078612270.5709414675071.28705412650.2419054794370.396789061737-0.0261529161654-0.476626313639-0.306977831902-0.114583843444-0.103628118433-0.2055112844020.07935133696020.4732793856390.0490145491021-0.002537586135240.5966422496320.06911723558530.5750324117223.6601742901814.0883551504-11.4349083645
30.411502823714-0.02418165716810.08234205999910.4221766190690.1287699395130.185662608324-0.0109190871725-0.01144720855660.006185842602940.0349044072506-0.01601399096130.007532894507480.005297177981930.01851317121680.007461858197490.172329226419-0.005455683192370.01003844239740.1803549099210.01895097675450.1670896762718.0586128874810.774015348129.463663963
40.142241450711-0.008011682101460.153714216970.1991439559470.07076848431920.187245066717-0.01398329613130.000953257595945-0.003073989711250.01680812968850.00526808289820.0333445812811-0.0256618941281-0.01073128014940.006657539875780.1715663243910.002034884608470.008640400312030.1699299681420.00708003970190.173220331923-2.334389438087.0564278154717.0130856342
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 383 through 453 )383 - 453383 - 453
22chain 'A' and (resid 454 through 508 )454 - 508454 - 508
33chain 'A' and (resid 1 through 200 )1 - 2001 - 200
44chain 'A' and (resid 201 through 382 )201 - 382201 - 382

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