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- PDB-7ykn: Crystal structure of (6-4) photolyase from Vibrio cholerae -

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Basic information

Entry
Database: PDB / ID: 7ykn
TitleCrystal structure of (6-4) photolyase from Vibrio cholerae
ComponentsCryptochrome/photolyase family protein
KeywordsLYASE / Photolyase / DNA repair / DMRL / [4Fe-4S] cluster / FAD
Function / homology
Function and homology information


4 iron, 4 sulfur cluster binding / lyase activity / nucleotide binding / metal ion binding
Similarity search - Function
Photolyase PhrB-like / : / Deoxyribodipyrimidine photo-lyase-related protein / Cryptochrome/DNA photolyase, FAD-binding domain-like superfamily / Rossmann-like alpha/beta/alpha sandwich fold
Similarity search - Domain/homology
Chem-DLZ / FLAVIN-ADENINE DINUCLEOTIDE / IMIDAZOLE / IRON/SULFUR CLUSTER / Cryptochrome/photolyase family protein
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsCakilkaya, B. / Kavakli, I.H. / DeMirci, H.
Funding support Turkey, 1items
OrganizationGrant numberCountry
Other government118C270 Turkey
CitationJournal: J.Biol.Chem. / Year: 2023
Title: The crystal structure of Vibrio cholerae (6-4) photolyase reveals interactions with cofactors and a DNA-binding region.
Authors: Cakilkaya, B. / Kavakli, I.H. / DeMirci, H.
History
DepositionJul 23, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 21, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 29, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)63,3867
Polymers61,6691
Non-polymers1,7176
Water10,034557
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1600 Å2
ΔGint-26 kcal/mol
Surface area19780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)200.751, 200.751, 77.023
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Cryptochrome/photolyase family protein / DNA photolyase / (6-4) photolyase


Mass: 61669.031 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria)
Gene: D6U24_03430, ERS013165_01011, ERS013186_03677, ERS013198_00016, ERS013199_00375, ERS013202_01140, ERS013207_00426
Production host: Escherichia coli (E. coli) / References: UniProt: A0A2V4NVF4

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Non-polymers , 6 types, 563 molecules

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


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#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-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
#5: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#6: 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
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 557 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.77 Å3/Da / Density % sol: 67.33 %
Crystal growTemperature: 277 K / Method: microbatch
Details: 5%(v/v) PEG400, 2 M ammonium citrate/citric acid pH 7.5, 1 M sodium sulfate decahydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU PhotonJet-R / Wavelength: 1.54 Å
DetectorType: RIGAKU HyPix-3000 / Detector: PIXEL / Date: Mar 10, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.5→24.62 Å / Num. obs: 32043 / % possible obs: 99.6 % / Redundancy: 60.4 % / Biso Wilson estimate: 15.97 Å2 / CC1/2: 0.955 / CC star: 0.988 / Rmerge(I) obs: 1.382 / Rpim(I) all: 0.1776 / Rrim(I) all: 1.394 / Net I/σ(I): 5.61
Reflection shellResolution: 2.5→2.58 Å / Rmerge(I) obs: 3.765 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 3130 / CC1/2: 0.546 / CC star: 0.84 / Rpim(I) all: 0.4855 / Rrim(I) all: 3.796 / % possible all: 99.97

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.20.1_4487refinement
PDB_EXTRACT3.27data extraction
CrysalisProdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4dja

4dja


Resolution: 2.5→24.62 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 25.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2832 1068 3.34 %
Rwork0.2254 30902 -
obs0.2274 31970 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 106.6 Å2 / Biso mean: 22.4624 Å2 / Biso min: 8.4 Å2
Refinement stepCycle: final / Resolution: 2.5→24.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4120 0 101 557 4778
Biso mean--17.61 24.49 -
Num. residues----507
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5-2.610.35051320.288737793911100
2.61-2.750.37251320.276838343966100
2.75-2.920.27951310.245437853916100
2.92-3.150.2961320.22738233955100
3.15-3.460.28641330.229338583991100
3.46-3.960.39211310.25943810394199
3.96-4.990.17961350.161739104045100
4.99-24.620.20751420.182641034245100
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)
11.42351.0558-0.46732.20290.20740.7126-0.0543-0.0641-0.15020.05730.0237-0.1815-0.43810.19040.05890.2095-0.10520.00780.1209-0.00140.1644-58.574340.7956-1.8303
20.78020.1475-0.02490.75980.09580.6288-0.04530.09960.1865-0.19060.124-0.0393-0.28150.2987-0.05190.1911-0.08460.0190.1651-0.00990.1923-58.594542.3785-5.0368
31.940.36090.83934.9897-1.88651.2104-0.21560.3847-0.2898-0.53270.1877-0.34540.31390.3074-0.00050.2319-0.01360.08440.1469-0.05870.2493-62.462614.7188-15.8401
41.0310.621-0.07820.7851-0.1140.7306-0.1227-0.1135-0.1341-0.14960.07730.42510.01740.10750.03340.1071-0.011-0.05080.0390.00450.1709-78.095620.20610.4475
51.07470.6419-0.34330.3649-0.1440.9068-0.02320.0620.0855-0.0672-0.02630.22020.01230.01930.0090.1157-0.0234-0.02010.0619-0.01490.1602-80.719326.72433.1789
61.1947-0.1370.20880.4572-0.04740.5948-0.06950.04050.0322-0.08850.0444-0.0153-0.0193-0.07160.02660.1554-0.0349-0.00970.0542-0.00840.1292-76.739523.7404-8.1268
72.94690.87730.12291.52120.14971.11050.00410.1608-0.1425-0.1734-0.00380.0111-0.0763-0.127-0.00250.13260.0087-0.02690.11260.01130.0922-86.11224.6351-15.7801
83.08620.90450.54853.33011.03445.4656-0.28170.6986-0.1287-0.31840.20510.01160.09510.15610.05970.2121-0.0448-0.03950.3386-0.01550.0976-96.238619.2665-28.4323
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 45 )A2 - 45
2X-RAY DIFFRACTION2chain 'A' and (resid 46 through 135 )A46 - 135
3X-RAY DIFFRACTION3chain 'A' and (resid 136 through 162 )A136 - 162
4X-RAY DIFFRACTION4chain 'A' and (resid 163 through 215 )A163 - 215
5X-RAY DIFFRACTION5chain 'A' and (resid 216 through 266 )A216 - 266
6X-RAY DIFFRACTION6chain 'A' and (resid 267 through 368 )A267 - 368
7X-RAY DIFFRACTION7chain 'A' and (resid 369 through 461 )A369 - 461
8X-RAY DIFFRACTION8chain 'A' and (resid 462 through 516 )A462 - 516

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