[English] 日本語
Yorodumi
- PDB-3vk8: Crystal structure of DNA-glycosylase bound to DNA containing Thym... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3vk8
TitleCrystal structure of DNA-glycosylase bound to DNA containing Thymine glycol
Components
  • DNA (5'-D(*CP*GP*TP*CP*CP*AP*(CTG)P*GP*TP*CP*TP*AP*C)-3')
  • DNA (5'-D(*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*G)-3')
  • Probable formamidopyrimidine-DNA glycosylase
KeywordsHYDROLASE/DNA / DNA glycosylase / hNEIL1 ortholog / DNA LESION / Thymine glycol / Zincless finger / DNA binding / HYDROLASE-DNA complex
Function / homology
Function and homology information


DNA-formamidopyrimidine glycosylase / 8-oxo-7,8-dihydroguanine DNA N-glycosylase activity / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / base-excision repair / damaged DNA binding / zinc ion binding
Similarity search - Function
: / Formamidopyrimidine-DNA glycosylase C-terminal domain / MutM-like, N-terminal / Formamidopyrimidine-DNA glycosylase H2TH domain / N-terminal domain of MutM-like DNA repair proteins / Formamidopyrimidine-DNA glycosylase N-terminal domain / Formamidopyrimidine-DNA glycosylase N-terminal domain / MutM-like, N-terminal / Formamidopyrimidine-DNA glycosylase, catalytic domain / Formamidopyrimidine-DNA glycosylase catalytic domain profile. ...: / Formamidopyrimidine-DNA glycosylase C-terminal domain / MutM-like, N-terminal / Formamidopyrimidine-DNA glycosylase H2TH domain / N-terminal domain of MutM-like DNA repair proteins / Formamidopyrimidine-DNA glycosylase N-terminal domain / Formamidopyrimidine-DNA glycosylase N-terminal domain / MutM-like, N-terminal / Formamidopyrimidine-DNA glycosylase, catalytic domain / Formamidopyrimidine-DNA glycosylase catalytic domain profile. / Formamidopyrimidine-DNA glycosylase H2TH domain / DNA glycosylase/AP lyase, H2TH DNA-binding / Helicase, Ruva Protein; domain 3 - #50 / Helicase, Ruva Protein; domain 3 / Ribosomal protein S13-like, H2TH / Alpha-Beta Barrel / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Probable formamidopyrimidine-DNA glycosylase
Similarity search - Component
Biological speciesAcanthamoeba polyphaga mimivirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2 Å
AuthorsImamura, K. / Averill, A. / Wallace, S.S. / Doublie, S.
Citation
Journal: J.Biol.Chem. / Year: 2012
Title: Structural characterization of viral ortholog of human DNA glycosylase NEIL1 bound to thymine glycol or 5-hydroxyuracil-containing DNA
Authors: Imamura, K. / Averill, A. / Wallace, S.S. / Doublie, S.
#1: Journal: J.Biol.Chem. / Year: 2009
Title: Structural characterization of a viral NEIL1 ortholog unliganded and bound to abasic site-containing DNA
Authors: Imamura, K. / Wallace, S.S. / Doublie, S.
History
DepositionNov 10, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 14, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 16, 2013Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _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: Probable formamidopyrimidine-DNA glycosylase
B: Probable formamidopyrimidine-DNA glycosylase
C: DNA (5'-D(*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*G)-3')
D: DNA (5'-D(*CP*GP*TP*CP*CP*AP*(CTG)P*GP*TP*CP*TP*AP*C)-3')
E: DNA (5'-D(*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*G)-3')
F: DNA (5'-D(*CP*GP*TP*CP*CP*AP*(CTG)P*GP*TP*CP*TP*AP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,1617
Polymers85,0696
Non-polymers921
Water7,999444
1
A: Probable formamidopyrimidine-DNA glycosylase
C: DNA (5'-D(*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*G)-3')
D: DNA (5'-D(*CP*GP*TP*CP*CP*AP*(CTG)P*GP*TP*CP*TP*AP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6274
Polymers42,5353
Non-polymers921
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4480 Å2
ΔGint-23 kcal/mol
Surface area16120 Å2
MethodPISA
2
B: Probable formamidopyrimidine-DNA glycosylase
E: DNA (5'-D(*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*G)-3')
F: DNA (5'-D(*CP*GP*TP*CP*CP*AP*(CTG)P*GP*TP*CP*TP*AP*C)-3')


Theoretical massNumber of molelcules
Total (without water)42,5353
Polymers42,5353
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4120 Å2
ΔGint-24 kcal/mol
Surface area16400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.737, 121.617, 80.836
Angle α, β, γ (deg.)90.000, 95.540, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Probable formamidopyrimidine-DNA glycosylase / Fapy-DNA glycosylase / DNA-(apurinic or apyrimidinic site) lyase / AP lyase


Mass: 34581.367 Da / Num. of mol.: 2 / Mutation: E3Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acanthamoeba polyphaga mimivirus / Gene: MIMI_L315 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)pLys
References: UniProt: Q5UQ00, DNA-formamidopyrimidine glycosylase, DNA-(apurinic or apyrimidinic site) lyase
#2: DNA chain DNA (5'-D(*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*G)-3')


Mass: 4016.623 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: complementary DNA
#3: DNA chain DNA (5'-D(*CP*GP*TP*CP*CP*AP*(CTG)P*GP*TP*CP*TP*AP*C)-3')


Mass: 3936.563 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: DNA containing Thymine glycol
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 444 / 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: 2.29 Å3/Da / Density % sol: 46.18 % / Description: The SF file contains Friedel pairs / Mosaicity: 0.49 °
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / pH: 6.3
Details: PEG 3350, Mg(NO3)2, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 285K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SYNCHROTRONAPS 23-ID-B11.0332
ROTATING ANODERIGAKU RUH3R21.5418
Detector
TypeIDDetectorDateDetails
MARMOSAIC 300 mm CCD1CCDOct 25, 2008mirrors
MAR scanner 345 mm plate2IMAGE PLATEAug 15, 2008Xenocs FOX 2D Multilayer mirrors
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1DOUBLE CRYSTAL CRYO-COOLED SI(111)SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.03321
21.54181
ReflectionResolution: 2→35 Å / Num. obs: 96852 / % possible obs: 94.2 % / Redundancy: 8 % / Biso Wilson estimate: 21.4 Å2 / Rmerge(I) obs: 0.133 / Χ2: 1.034 / Net I/σ(I): 6.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2-2.072.80.3737750.5461,273.3
2.07-2.153.20.34640420.4811,279.7
2.15-2.254.30.38245390.8141,288.4
2.25-2.3780.33651210.5871,2100
2.37-2.529.10.30951460.5411,2100
2.52-2.719.70.25851260.5911,2100
2.71-2.999.90.18251520.7071,2100
2.99-3.4210.10.12751271.1651,2100
3.42-4.3110.10.09551831.851,2100
4.31-35100.07752151.8551,2100

-
Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
CNS1.2refinement
PDB_EXTRACT3.1data extraction
DENZOdata reduction
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2→14.96 Å / Occupancy max: 1 / Occupancy min: 0 / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: The SF file contains Friedel pairs
RfactorNum. reflection% reflectionSelection details
Rfree0.2304 8303 8.2 %from 3A46
Rwork0.1998 ---
all0.211 ---
obs0.201 88772 87.2 %-
Solvent computationBsol: 69.5923 Å2
Displacement parametersBiso max: 56.57 Å2 / Biso mean: 21.482 Å2 / Biso min: 3.16 Å2
Baniso -1Baniso -2Baniso -3
1-4.062 Å20 Å20.584 Å2
2---5.424 Å20 Å2
3---1.362 Å2
Refinement stepCycle: LAST / Resolution: 2→14.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4732 1054 6 444 6236
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_d1.165
X-RAY DIFFRACTIONc_mcbond_it1.371.5
X-RAY DIFFRACTIONc_scbond_it2.0572
X-RAY DIFFRACTIONc_mcangle_it2.1392
X-RAY DIFFRACTIONc_scangle_it3.0672.5
LS refinement shellResolution: 2→2.13 Å
RfactorNum. reflection% reflection
Rfree0.297 831 -
Rwork0.269 --
obs-9229 54.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.paramCNS_TOPPAR:protein.top
X-RAY DIFFRACTION2dna-rna_rep-090403.paramdna-rna-test.top
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.paramCNS_TOPPAR:water.top
X-RAY DIFFRACTION4CNS_TOPPAR:ion.paramCNS_TOPPAR:ion.top
X-RAY DIFFRACTION5gol_xplor_paramgol_xplor_top

+
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://pdbjlvh1.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