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- PDB-2wb2: Drosophila Melanogaster (6-4) Photolyase Bound To double stranded... -

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Basic information

Entry
Database: PDB / ID: 2wb2
TitleDrosophila Melanogaster (6-4) Photolyase Bound To double stranded Dna containing a T(6-4)C Photolesion
Components
  • 5'-D(*AP*CP*AP*GP*CP*GP*GP*64PP*ZP*GP*CP*AP *GP*GP*T)-3'
  • 5'-D(*TP*AP*CP*CP*TP*GP*CP*GP*AP*CP*CP*GP*CP*TP*G)-3'
  • PHOTOLYASE
KeywordsLYASE/DNA / LYASE-DNA COMPLEX / PHOTOLESION / DNA PHOTOLYASE / 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
DNA Cyclobutane Dipyrimidine Photolyase, subunit A; domain 3 / DNA Cyclobutane Dipyrimidine Photolyase, subunit A, domain 3 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #80 / 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. ...DNA Cyclobutane Dipyrimidine Photolyase, subunit A; domain 3 / DNA Cyclobutane Dipyrimidine Photolyase, subunit A, domain 3 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #80 / 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)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsGlas, A.F. / Schneider, S. / Maul, M.J. / Hennecke, U. / Carell, T.
Citation
Journal: Chemistry / Year: 2009
Title: Crystal Structure of the T(6-4)C Lesion in Complex with a (6-4) DNA Photolyase and Repair of Uv- Induced (6-4) and Dewar Photolesions.
Authors: Glas, A.F. / Schneider, S. / Maul, M.J. / Hennecke, U. / Carell, T.
#1: Journal: Angew.Chem.Int.Ed.Engl. / Year: 2008
Title: Crystal Structure and Mechanism of a DNA (6-4) Photolyase.
Authors: Maul, M.J. / Barends, T.R.M. / Glas, A.F. / Cryle, M.J. / Domratcheva, T. / Schneider, S. / Schlichting, I. / Carell, T.
History
DepositionFeb 20, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 26, 2011Group: Database references / Source and taxonomy / Structure summary
Revision 1.3May 29, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other / Source and taxonomy
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_entity_src_syn / pdbx_seq_map_depositor_info / struct_biol / struct_conn
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval ..._exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _pdbx_seq_map_depositor_info.one_letter_code_mod / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Aug 7, 2019Group: Data collection / Experimental preparation / Category: chem_comp / exptl_crystal_grow
Item: _chem_comp.type / _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.5Oct 16, 2019Group: Data collection / Other / Category: pdbx_database_status / reflns_shell
Item: _pdbx_database_status.status_code_sf / _reflns_shell.Rmerge_I_obs
Revision 2.0Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Polymer sequence / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_poly / 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 / _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: PHOTOLYASE
C: 5'-D(*AP*CP*AP*GP*CP*GP*GP*64PP*ZP*GP*CP*AP *GP*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)72,8794
Polymers72,0933
Non-polymers7861
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5300 Å2
ΔGint-19.86 kcal/mol
Surface area25750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.550, 89.000, 91.670
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 PHOTOLYASE / DNA PHOTOLYASE / RE11660P


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: DERIVED FROM PDEST007 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K-12 / Variant (production host): ROSETTA-GAMI PLYSS (DE3)
References: UniProt: Q8SXK5, deoxyribodipyrimidine photo-lyase
#2: DNA chain 5'-D(*AP*CP*AP*GP*CP*GP*GP*64PP*ZP*GP*CP*AP *GP*GP*T)-3'


Mass: 4637.026 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: 6-4 LINK BETWEEN T 8 AND C 8 (SEE REMARK 600) / Source: (synth.) synthetic construct (others)
#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 / Source: (synth.) synthetic construct (others)
#4: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
Nonpolymer detailsCHAIN C HETEROGENS 64P AND Z: RESIDUES DT 8 AND DC 9 HAVE FORMED A PHOTOPRODUCT BY THE COVALENT ...CHAIN C HETEROGENS 64P AND Z: RESIDUES DT 8 AND DC 9 HAVE FORMED A PHOTOPRODUCT BY THE COVALENT BONDING OF ATOM C6 OF 64P TO C4 OF Z.
Sequence detailsCONSTRUCT CONTAINS RESIDUES 1-520

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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: 2.48 Å3/Da / Density % sol: 50 % / Description: NONE
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: PROTEIN WAS MIXED WITH DNA IN A 1:1.1 MOLAR RATIO WITH A FINAL CONCENTRATION OF 8.5MG/ML PROTEIN. 0.1M HEPES PH 7, 15-20% POLYETHYLENGLYCOL 4000, HANGING-DROP VAPOUR DIFFUSION

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.076
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 4, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.076 Å / Relative weight: 1
ReflectionResolution: 2.95→45.8 Å / Num. obs: 15653 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 5.3 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 13.1
Reflection shellResolution: 2.95→3.11 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 3.1 / % possible all: 100

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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: 2.95→45 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.912 / SU B: 38.342 / SU ML: 0.337 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.415 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.24252 774 5 %RANDOM
Rwork0.20354 ---
obs0.20554 14835 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 63.264 Å2
Baniso -1Baniso -2Baniso -3
1-4 Å20 Å20 Å2
2---2.4 Å20 Å2
3----1.6 Å2
Refinement stepCycle: LAST / Resolution: 2.95→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4162 608 53 0 4823
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0225023
X-RAY DIFFRACTIONr_bond_other_d0.0070.023317
X-RAY DIFFRACTIONr_angle_refined_deg1.4912.126952
X-RAY DIFFRACTIONr_angle_other_deg0.8793.0018035
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7745507
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.40323.14207
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.31415735
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8361534
X-RAY DIFFRACTIONr_chiral_restr0.0750.2729
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215062
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02973
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_it0.4121.52546
X-RAY DIFFRACTIONr_mcbond_other0.0881.51008
X-RAY DIFFRACTIONr_mcangle_it0.80624125
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.33532477
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.1914.52827
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: 2.95→3.026 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.434 62 -
Rwork0.34 1067 -
obs--100 %
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)
11.45650.91460.14712.586-0.0281.7623-0.08250.22230.1351-0.26180.03360.0071-0.07160.07160.04890.41270.00790.04420.338-0.00150.268614.504917.86194.2747
21.53270.5952-0.35861.156-0.96110.8609-0.02440.06450.1345-0.0583-0.01690.0674-0.02560.0620.04130.36510.03180.00680.2325-0.0080.33267.367816.595612.2401
34.6003-0.994-0.87462.311-0.09721.25510.00620.04670.0587-0.01030.0071-0.0289-0.03740.0972-0.01330.4155-0.0061-0.00140.39110.01170.378513.352326.8889-3.3677
41.83781.6810.60454.0237-0.49490.67720.01620.08540.2055-0.35940.02710.22370.14990.1076-0.04330.5001-0.00450.03350.41330.00370.330211.259614.4349-7.5215
50.46190.0767-0.15831.3123-0.12742.03540.01220.1827-0.0703-0.1994-0.0296-0.24310.10020.0530.01750.37820.030.05010.3645-0.02950.343914.5833-7.1784-5.6853
60.2390.4391-0.19661.6639-0.05840.44940.05750.02720.10390.0446-0.0741-0.0197-0.09150.02320.01650.33310.03-0.00480.32620.01160.32199.119512.777215.0841
71.69580.101-0.47431.54970.18561.3679-0.0348-0.0404-0.1117-0.12970.0284-0.1090.13330.21610.00640.32490.0314-0.00750.2874-0.00430.283510.2848-9.97812.7764
80.80280.0841-0.22970.561-0.28831.02930.01350.1666-0.0127-0.12380.02090.06290.0059-0.0745-0.03440.34540.0139-0.0290.288-0.0270.2922-10.4676-6.14013.0418
90.27980.2941-0.3832.26450.8172.57290.02370.22110.0418-0.0491-0.0615-0.0405-0.0852-0.12530.03780.32220.031-0.0280.3515-0.00440.2909-5.592-4.97751.4349
101.11270.5651-0.29220.7299-0.71652.5753-0.03650.0551-0.09190.1055-0.02270.18210.2705-0.13530.05920.31370.00170.0060.2552-0.03430.3256-15.1184-15.21319.1148
111.1127-0.0615-1.51330.0364-0.10455.1376-0.01850.0035-0.04330.03040.04910.07880.1787-0.1235-0.03060.3399-0.01510.00250.3724-0.02880.4104-28.2157-13.270418.9111
120.82180.3796-1.20771.4288-1.37444.823-0.06160.1142-0.0766-0.1419-0.018-0.08620.04220.03330.07960.3942-0.0143-0.0250.3806-0.01810.3914-15.083-18.6472-10.2159
133.79461.5748-0.58553.92850.17891.80980.05980.2259-0.1824-0.27190.15180.26350.3223-0.3699-0.21160.48080.01650.01730.4986-0.0470.46131.2916-31.0778-17.7192
144.25850.91690.95310.625-0.65792.1021-0.11280.3683-0.2334-0.21010.1244-0.12010.52480.1327-0.01160.48120.01960.00320.3279-0.03790.3604-0.0823-26.3654-1.4874
155.6026-1.88972.58840.6786-0.84171.25770.0919-0.7621-0.92520.080.31860.40210.1299-0.1911-0.41050.59050.14340.05980.55010.07520.5145-11.4363-32.951613.373
162.79131.51012.65742.16930.64174.1150.07980.2733-0.1669-0.18090.1089-0.2126-0.13720.3328-0.18870.49080.00980.00290.49750.0190.461-1.9494-33.452514.0949
171.9866-0.46642.17541.2324-1.20518.43790.06990.3890.047-0.3887-0.01940.0527-0.11210.0818-0.05050.46380.00530.01080.4468-0.00830.4789-12.0846-32.2375-0.8255
180.165-0.50890.38215.9617-1.34880.96420.10730.147-0.0413-0.12710.0081-0.12220.20730.1714-0.11540.47440.04040.06130.5423-0.07590.28572.2209-24.0761-12.0191
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 56
2X-RAY DIFFRACTION2A57 - 90
3X-RAY DIFFRACTION3A91 - 104
4X-RAY DIFFRACTION4A105 - 134
5X-RAY DIFFRACTION5A135 - 173
6X-RAY DIFFRACTION6A174 - 242
7X-RAY DIFFRACTION7A243 - 301
8X-RAY DIFFRACTION8A302 - 385
9X-RAY DIFFRACTION9A386 - 418
10X-RAY DIFFRACTION10A419 - 457
11X-RAY DIFFRACTION11A458 - 486
12X-RAY DIFFRACTION12A487 - 509
13X-RAY DIFFRACTION13C1 - 4
14X-RAY DIFFRACTION14C5 - 10
15X-RAY DIFFRACTION15C11 - 15
16X-RAY DIFFRACTION16D1 - 5
17X-RAY DIFFRACTION17D6 - 9
18X-RAY DIFFRACTION18D10 - 15

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