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- PDB-2wq6: Structure of the 6-4 photolyase of D. melanogaster in complex wit... -

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Basic information

Entry
Database: PDB / ID: 2wq6
TitleStructure of the 6-4 photolyase of D. melanogaster in complex with the non-natural N4-methyl T(Dewar)C lesion
Components
  • 5'-D(*AP*CP*AP*GP*CP*GP*GP*TDYP*CDWP*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: 2.3 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 / Refinement description / Version format compliance
Revision 1.2May 8, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_seq_map_depositor_info / struct_conn
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval ..._exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _pdbx_seq_map_depositor_info.one_letter_code_mod / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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*CDWP*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
Water3,063170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5490 Å2
ΔGint-13.9 kcal/mol
Surface area25640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.169, 87.486, 91.856
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*CDWP*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.: 170 / 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 growTemperature: 291 K / Details: 100 MM HEPES, PH 7, 13-17% PEG1500, 18C

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / 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: 2.3→43.73 Å / Num. obs: 32351 / % possible obs: 99.3 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Biso Wilson estimate: 42.4 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 18.1
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 3.9 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.5.0070refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3CVU

3cvu


Resolution: 2.3→43.74 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.926 / SU B: 6.078 / SU ML: 0.148 / Cross valid method: THROUGHOUT / ESU R: 0.323 / ESU R Free: 0.216 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. RESIDUES DT 8 AND DC 9 HAVE FORMED THE DEWAR VALENCE ISOMER OF THE 6-4 PHOTOPRODUCT BY AND ARE COVALENTLY ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. RESIDUES DT 8 AND DC 9 HAVE FORMED THE DEWAR VALENCE ISOMER OF THE 6-4 PHOTOPRODUCT BY AND ARE COVALENTLY BONDED BETWEEN ATOM C6 TDY AND ATOM C4 OF CDW
RfactorNum. reflection% reflectionSelection details
Rfree0.22848 1620 5 %RANDOM
Rwork0.20129 ---
obs0.20265 30688 99.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.233 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2--0.88 Å20 Å2
3----0.9 Å2
Refinement stepCycle: LAST / Resolution: 2.3→43.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4162 609 53 170 4994
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0225039
X-RAY DIFFRACTIONr_bond_other_d0.0050.023333
X-RAY DIFFRACTIONr_angle_refined_deg1.222.1286976
X-RAY DIFFRACTIONr_angle_other_deg0.9333.0018067
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9985509
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.49323.014209
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.92815737
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6191536
X-RAY DIFFRACTIONr_chiral_restr0.1030.2730
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215081
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02982
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0411.52552
X-RAY DIFFRACTIONr_mcbond_other0.2211.51010
X-RAY DIFFRACTIONr_mcangle_it1.95924136
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.68532487
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.1274.52836
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 118 -
Rwork0.271 2236 -
obs--99.53 %

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