[English] 日本語
Yorodumi
- PDB-2wq7: Structure of the 6-4 photolyase of D. melanogaster in complex wit... -

+
Open data


ID or keywords:

Loading...

-
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
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)
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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 / 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 / Water


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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more