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- PDB-9q8f: Structure of the (6-4) photolyase of Caulobacter crescentus with ... -

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Basic information

Entry
Database: PDB / ID: 9q8f
TitleStructure of the (6-4) photolyase of Caulobacter crescentus with K48A mutation in its dark adapted and oxidized state determined by 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: 1.5 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
DepositionFeb 24, 2025Deposition 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)60,23513
Polymers58,0631
Non-polymers2,17212
Water11,367631
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3270 Å2
ΔGint-61 kcal/mol
Surface area20520 Å2
Unit cell
Length a, b, c (Å)48.984, 102.102, 102.944
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

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Protein , 1 types, 1 molecules A

#1: Protein Cryptochrome/photolyase family protein


Mass: 58063.184 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caulobacter vibrioides (bacteria) / Gene: CC_0646 / Plasmid: pET28a / Production host: Escherichia coli B (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Gold / References: UniProt: Q9AAF5

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Non-polymers , 8 types, 643 molecules

#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: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 631 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.22 Å3/Da / Density % sol: 44.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1 M Tris, pH7.0 0.2M MgCl2 25% (w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.87 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 2, 2024
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 1.5→45.96 Å / Num. obs: 82472 / % possible obs: 98.69 % / Redundancy: 11.9 % / Biso Wilson estimate: 12.81 Å2 / CC1/2: 0.993 / CC star: 0.998 / Rmerge(I) obs: 0.0907 / Rpim(I) all: 0.02792 / Rrim(I) all: 0.09506 / Net I/σ(I): 21.94
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 11.4 % / Rmerge(I) obs: 0.6294 / Mean I/σ(I) obs: 4.95 / Num. unique obs: 7750 / CC1/2: 0.905 / CC star: 0.975 / Rpim(I) all: 0.191 / Rrim(I) all: 0.6584 / % possible all: 94.29

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→45.96 Å / SU ML: 0.1112 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 14.5334
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1646 4063 4.94 %
Rwork0.138 78161 -
obs0.1393 82224 98.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.29 Å2
Refinement stepCycle: LAST / Resolution: 1.5→45.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4079 0 127 631 4837
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00864494
X-RAY DIFFRACTIONf_angle_d1.00336121
X-RAY DIFFRACTIONf_chiral_restr0.054619
X-RAY DIFFRACTIONf_plane_restr0.0122800
X-RAY DIFFRACTIONf_dihedral_angle_d9.3253638
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.520.23591280.20662339X-RAY DIFFRACTION87.23
1.52-1.540.19481520.1972660X-RAY DIFFRACTION98.67
1.54-1.560.21751220.19022675X-RAY DIFFRACTION98.94
1.56-1.580.23241470.18322708X-RAY DIFFRACTION99.1
1.58-1.60.18641400.17692617X-RAY DIFFRACTION99.28
1.6-1.620.19491540.16942659X-RAY DIFFRACTION99.01
1.62-1.650.17281280.1652703X-RAY DIFFRACTION99.09
1.65-1.670.17391480.15792639X-RAY DIFFRACTION99.18
1.67-1.70.20221370.15082708X-RAY DIFFRACTION99.27
1.7-1.730.18671250.14892687X-RAY DIFFRACTION99.26
1.73-1.760.17051500.14172689X-RAY DIFFRACTION99.44
1.76-1.790.16341310.14052691X-RAY DIFFRACTION99.4
1.79-1.830.19541390.13882672X-RAY DIFFRACTION99.36
1.83-1.870.15911770.13742663X-RAY DIFFRACTION98.89
1.87-1.910.16971280.13742673X-RAY DIFFRACTION98.7
1.91-1.960.1831510.13812700X-RAY DIFFRACTION98.79
1.96-2.010.15311540.13492648X-RAY DIFFRACTION98.98
2.01-2.070.1781030.13292726X-RAY DIFFRACTION98.99
2.07-2.140.14531430.12962696X-RAY DIFFRACTION98.85
2.14-2.220.14651450.12782708X-RAY DIFFRACTION99.03
2.22-2.310.1391440.12692673X-RAY DIFFRACTION99.3
2.31-2.410.16061290.12212746X-RAY DIFFRACTION99.65
2.41-2.540.15391550.12062735X-RAY DIFFRACTION99.9
2.54-2.70.13931470.12212739X-RAY DIFFRACTION99.9
2.7-2.90.15131520.12212751X-RAY DIFFRACTION99.76
2.91-3.20.14931480.122735X-RAY DIFFRACTION99.52
3.2-3.660.14421220.12072775X-RAY DIFFRACTION98.57
3.66-4.610.16371320.11792808X-RAY DIFFRACTION99.22
4.61-45.960.18441320.17822938X-RAY DIFFRACTION98.49
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)
10.3607260528430.0369497985477-0.19404306680.418283611283-0.1486249375790.367423291978-0.01715645495710.1097769429950.0532054619923-0.1757487547770.03870137078650.0798378302666-0.0452710342222-0.109920683985-1.23336023686E-50.15808975891-0.00672885361994-0.01898693745460.1171846289690.004226688724370.133362044836-8.2996449079617.9868508989-36.1963277189
20.079885096093-0.004321494839840.02621863155130.05460163224680.01968758546230.0156728551002-0.0203800603467-0.1053098010370.02053455034310.08871599026680.05856370587170.166933127868-0.00240033660333-0.154435629168-2.09697273833E-50.1296795421590.003456611586330.03104827804120.170067285148-0.02016765831130.188932528672-19.8632718136-1.76191005946-14.6522985468
30.4004694328610.299145512904-0.1479803353130.272562719017-0.09573914905330.1576318222710.0527813817465-0.169275719693-0.08680932582840.023504229858-0.135328927462-0.1027026139550.06506996616610.132744983862-0.01412069866250.137979618543-0.01106608967920.03042023243890.1582661005230.01927544503930.1822337136761.17676238016-8.02331524347-14.2543012582
40.320385304494-0.06494317591020.09385351258770.1230057534010.04765201396290.1520046297370.0314428533944-0.01978394057010.0281073511421-0.0561325620136-0.0214882082443-0.110995616876-0.003116177602790.112726620899-1.05158375639E-60.137396497468-0.01731786551980.02013793974820.114463267231-0.01018346082110.1484253153139.747608715187.07078146999-22.6799827418
50.08664269292890.00540456336327-0.009322934423150.0752079194377-0.04138895124440.0428222747590.0006628895812850.0187626318017-0.0507547923551-0.03709967467280.007586829915750.0006203326671110.04130279705350.02720356965111.4621377716E-50.1147774154570.008695446718370.003233095427910.0848214325813-0.01619597880170.11759884818-1.94114426391-6.0334968329-21.8019080722
60.3519377521580.1799619116620.0526040894030.4161648842030.07915072620660.4299595089370.0579806025755-0.1792677792820.1205727868340.0796717210954-0.07857731478930.02765823948390.0146166001149-0.0132789847546-0.00236555362520.0906646366222-0.01718943739840.01913470139550.115800468607-0.04079468547330.105507960652-2.2179385973112.6564974257-7.86562008037
70.211990745372-0.0696997614698-0.02554277732580.0711223679184-0.04464494713970.0707672501028-0.0185089139085-0.1741020854010.0526428883080.138792820739-0.05332596986960.00101024487547-0.012148621216-0.072032410656-0.2917796875410.199165387414-0.1074703754830.008777267332260.321969779861-0.1120527665920.03261317707274.9431479744212.259689375610.1559864828
80.109164388186-0.02137561297860.1574115766820.0131208628124-0.05491002837450.2938862386040.0233979645653-0.278925567330.02473713577360.1480901233450.01663225348910.01558265724210.229632467338-0.3356617325560.6135067854850.318280197902-0.1710545298130.06626362690150.479272456592-0.1344032761790.139986655069-5.3724118828813.303115654412.1644162958
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 134 )1 - 1341 - 134
22chain 'A' and (resid 135 through 161 )135 - 161135 - 161
33chain 'A' and (resid 162 through 200 )162 - 200162 - 200
44chain 'A' and (resid 201 through 262 )201 - 262201 - 262
55chain 'A' and (resid 263 through 307 )263 - 307263 - 307
66chain 'A' and (resid 308 through 439 )308 - 439308 - 439
77chain 'A' and (resid 440 through 465 )440 - 465440 - 465
88chain 'A' and (resid 466 through 509 )466 - 509466 - 509

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