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- PDB-2wq7: Structure of the 6-4 photolyase of D. melanogaster in complex wit... -

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Basic information

Entry
Database: PDB / ID: 2wq7
TitleStructure of the 6-4 photolyase of D. melanogaster in complex with the non-natural N4-methyl T(6-4)C lesion
Components
  • 5'-D(*AP*CP*AP*GP*CP*GP*GP*TDYP*ZP*GP* CP*AP*AP*GP*T)-3'
  • 5'-D(*TP*AP*CP*CP*TP*GP*CP*GP*AP*CP* CP*GP*CP*TP*G)-3'
  • RE11660P
KeywordsLYASE/DNA / LYASE-DNA COMPLEX / DNA REPAIR / DNA LESION / LYASE
Function / homology
Function and homology information


deoxyribodipyrimidine photo-lyase activity / entrainment of circadian clock by photoperiod / FAD binding / circadian regulation of gene expression / DNA binding / nucleus / cytoplasm
Similarity search - Function
Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #80 / DNA Cyclobutane Dipyrimidine Photolyase, subunit A; domain 3 / DNA Cyclobutane Dipyrimidine Photolyase, subunit A, domain 3 / Cryptochrome/DNA photolyase class 1 / Cryptochrome/DNA photolyase, FAD-binding domain / FAD binding domain of DNA photolyase / DNA photolyase, N-terminal / Cryptochrome/photolyase, N-terminal domain superfamily / DNA photolyase / Photolyase/cryptochrome alpha/beta domain profile. ...Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #80 / DNA Cyclobutane Dipyrimidine Photolyase, subunit A; domain 3 / DNA Cyclobutane Dipyrimidine Photolyase, subunit A, domain 3 / Cryptochrome/DNA photolyase class 1 / Cryptochrome/DNA photolyase, FAD-binding domain / FAD binding domain of DNA photolyase / DNA photolyase, N-terminal / Cryptochrome/photolyase, N-terminal domain superfamily / DNA photolyase / Photolyase/cryptochrome alpha/beta domain profile. / Cryptochrome/DNA photolyase, FAD-binding domain-like superfamily / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / DNA / DNA (> 10) / RE11660p
Similarity search - Component
Biological speciesDROSOPHILA MELANOGASTER (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsGlas, A.F. / Kaya, E. / Schneider, S. / Maul, M.J. / Carell, T.
CitationJournal: J.Am.Chem.Soc. / Year: 2010
Title: DNA (6-4) Photolyases Reduce Dewar Isomers for Isomerization Into (6-4) Lesions.
Authors: Glas, A.F. / Kaya, E. / Schneider, S. / Heil, K. / Fazio, D. / Maul, M.J. / Carell, T.
History
DepositionAug 14, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 23, 2010Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2011Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Refinement description / Version format compliance
Revision 2.0Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Polymer sequence / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_poly / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RE11660P
C: 5'-D(*AP*CP*AP*GP*CP*GP*GP*TDYP*ZP*GP* CP*AP*AP*GP*T)-3'
D: 5'-D(*TP*AP*CP*CP*TP*GP*CP*GP*AP*CP* CP*GP*CP*TP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,8934
Polymers72,1073
Non-polymers7861
Water7,260403
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5490 Å2
ΔGint-16.6 kcal/mol
Surface area25660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.786, 89.265, 91.491
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein RE11660P / 6-4 DNA PHOTOLYASE


Mass: 62910.137 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-520
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DROSOPHILA MELANOGASTER (fruit fly) / Plasmid: PDEST007 DERIVATIVE / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA-GAMI PLYSS (DE3)
References: UniProt: Q8SXK5, deoxyribodipyrimidine photo-lyase
#2: DNA chain 5'-D(*AP*CP*AP*GP*CP*GP*GP*TDYP*ZP*GP* CP*AP*AP*GP*T)-3'


Mass: 4651.054 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain 5'-D(*TP*AP*CP*CP*TP*GP*CP*GP*AP*CP* CP*GP*CP*TP*G)-3'


Mass: 4545.948 Da / Num. of mol.: 1 / Source method: obtained synthetically
#4: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 403 / Source method: isolated from a natural source / Formula: H2O

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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: 2.95 Å3/Da / Density % sol: 58 % / Description: NONE
Crystal growDetails: 100MM HEPES PH 7, 13-17% PEG1500 18DGC

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 27, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→40.5 Å / Num. obs: 48536 / % possible obs: 99.2 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Biso Wilson estimate: 26.67 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 14.7
Reflection shellResolution: 2→2.1 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 3.7 / % possible all: 96.2

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3CVU

3cvu


Resolution: 2→40.468 Å / SU ML: 0.43 / σ(F): 1.35 / Phase error: 19.97 / Stereochemistry target values: ML
Details: RESIDUES DT 8 AND DC 9 HAVE FORMED A 6-4 PHOTOPRODUCT BY THE COVALENT BONDING OF ATOM C6 OF TDY TO C4 OF Z.
RfactorNum. reflection% reflection
Rfree0.2089 2451 5.1 %
Rwork0.1778 --
obs0.1794 48536 99.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40 Å2 / ksol: 0.351 e/Å3
Displacement parametersBiso mean: 28.4 Å2
Baniso -1Baniso -2Baniso -3
1-0.8264 Å20 Å20 Å2
2--0.8688 Å20 Å2
3----3.1512 Å2
Refinement stepCycle: LAST / Resolution: 2→40.468 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4162 609 53 403 5227
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115058
X-RAY DIFFRACTIONf_angle_d1.3777002
X-RAY DIFFRACTIONf_dihedral_angle_d19.0711938
X-RAY DIFFRACTIONf_chiral_restr0.103727
X-RAY DIFFRACTIONf_plane_restr0.007790
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9955-2.03380.30231350.23612307X-RAY DIFFRACTION90
2.0338-2.07540.29561170.22222546X-RAY DIFFRACTION99
2.0754-2.12050.25681360.19212519X-RAY DIFFRACTION100
2.1205-2.16980.23561210.17912574X-RAY DIFFRACTION100
2.1698-2.22410.211470.17812517X-RAY DIFFRACTION100
2.2241-2.28420.20811490.18222554X-RAY DIFFRACTION100
2.2842-2.35140.2561440.17792530X-RAY DIFFRACTION100
2.3514-2.42730.24131230.17552558X-RAY DIFFRACTION100
2.4273-2.5140.23681550.17352535X-RAY DIFFRACTION100
2.514-2.61470.21211560.17922559X-RAY DIFFRACTION100
2.6147-2.73360.27551240.18762565X-RAY DIFFRACTION100
2.7336-2.87770.25321340.20072584X-RAY DIFFRACTION100
2.8777-3.0580.23831280.19712576X-RAY DIFFRACTION100
3.058-3.2940.20991300.18592597X-RAY DIFFRACTION100
3.294-3.62530.18741340.16852600X-RAY DIFFRACTION100
3.6253-4.14940.16551370.14362623X-RAY DIFFRACTION100
4.1494-5.2260.1491410.14082616X-RAY DIFFRACTION99
5.226-40.47610.16151400.16232725X-RAY DIFFRACTION98

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