[English] 日本語
Yorodumi
- PDB-7n3y: Crystal Structure of Saccharomyces cerevisiae Apn2 Catalytic Doma... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7n3y
TitleCrystal Structure of Saccharomyces cerevisiae Apn2 Catalytic Domain E59Q/D222N Mutant in Complex with DNA
Components
  • DNA (5'-D(*CP*CP*GP*AP*AP*AP*TP*TP*(PST)P*(SC)P*(GS)P*(GS)P*(AS))-3')
  • DNA (5'-D(*TP*CP*CP*GP*AP*AP*AP*TP*(PST)P*(PST)P*(SC)P*(GS)P*(GS))-3')
  • DNA-(apurinic or apyrimidinic site) endonuclease 2
KeywordsHYDROLASE/DNA / nuclease / DNA complex / EEP fold / APE2 homolog / HYDROLASE / HYDROLASE-DNA complex
Function / homology
Function and homology information


double-stranded DNA 3'-5' DNA exonuclease activity / exodeoxyribonuclease III / phosphoric diester hydrolase activity / DNA-(apurinic or apyrimidinic site) endonuclease activity / 3'-5' exonuclease activity / base-excision repair / endonuclease activity / DNA binding / zinc ion binding / nucleus
Similarity search - Function
Zinc finger, GRF-type / GRF zinc finger / Zinc finger GRF-type profile. / AP endonuclease 1, conserved site / AP endonucleases family 1 signature 3. / AP endonuclease 1 / AP endonucleases family 1 profile. / Deoxyribonuclease I; Chain A / Endonuclease/exonuclease/phosphatase / Endonuclease/exonuclease/phosphatase ...Zinc finger, GRF-type / GRF zinc finger / Zinc finger GRF-type profile. / AP endonuclease 1, conserved site / AP endonucleases family 1 signature 3. / AP endonuclease 1 / AP endonucleases family 1 profile. / Deoxyribonuclease I; Chain A / Endonuclease/exonuclease/phosphatase / Endonuclease/exonuclease/phosphatase / Endonuclease/Exonuclease/phosphatase family / Endonuclease/exonuclease/phosphatase superfamily / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / D(-)-TARTARIC ACID / L(+)-TARTARIC ACID / DNA / DNA (> 10) / DNA-(apurinic or apyrimidinic site) endonuclease 2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.73 Å
AuthorsWojtaszek, J.L. / Krahn, J. / Wallace, B.D. / Williams, R.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)1Z01ES102765 United States
CitationJournal: Cell Rep / Year: 2022
Title: Molecular basis for processing of topoisomerase 1-triggered DNA damage by Apn2/APE2.
Authors: Williams, J.S. / Wojtaszek, J.L. / Appel, D.C. / Krahn, J. / Wallace, B.D. / Walsh, E. / Kunkel, T.A. / Williams, R.S.
History
DepositionJun 2, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA-(apurinic or apyrimidinic site) endonuclease 2
B: DNA-(apurinic or apyrimidinic site) endonuclease 2
C: DNA-(apurinic or apyrimidinic site) endonuclease 2
D: DNA-(apurinic or apyrimidinic site) endonuclease 2
E: DNA (5'-D(*TP*CP*CP*GP*AP*AP*AP*TP*(PST)P*(PST)P*(SC)P*(GS)P*(GS))-3')
F: DNA (5'-D(*TP*CP*CP*GP*AP*AP*AP*TP*(PST)P*(PST)P*(SC)P*(GS)P*(GS))-3')
G: DNA (5'-D(*TP*CP*CP*GP*AP*AP*AP*TP*(PST)P*(PST)P*(SC)P*(GS)P*(GS))-3')
H: DNA (5'-D(*CP*CP*GP*AP*AP*AP*TP*TP*(PST)P*(SC)P*(GS)P*(GS)P*(AS))-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)206,38015
Polymers205,4858
Non-polymers8957
Water1,802100
1
A: DNA-(apurinic or apyrimidinic site) endonuclease 2
B: DNA-(apurinic or apyrimidinic site) endonuclease 2
E: DNA (5'-D(*TP*CP*CP*GP*AP*AP*AP*TP*(PST)P*(PST)P*(SC)P*(GS)P*(GS))-3')
F: DNA (5'-D(*TP*CP*CP*GP*AP*AP*AP*TP*(PST)P*(PST)P*(SC)P*(GS)P*(GS))-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,3329
Polymers102,7384
Non-polymers5945
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: DNA-(apurinic or apyrimidinic site) endonuclease 2
D: DNA-(apurinic or apyrimidinic site) endonuclease 2
G: DNA (5'-D(*TP*CP*CP*GP*AP*AP*AP*TP*(PST)P*(PST)P*(SC)P*(GS)P*(GS))-3')
H: DNA (5'-D(*CP*CP*GP*AP*AP*AP*TP*TP*(PST)P*(SC)P*(GS)P*(GS)P*(AS))-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,0476
Polymers102,7474
Non-polymers3002
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.408, 101.473, 144.973
Angle α, β, γ (deg.)90.00, 90.14, 90.00
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
DNA-(apurinic or apyrimidinic site) endonuclease 2 / AP endonuclease 2 / Apurinic-apyrimidinic endonuclease 2


Mass: 47322.094 Da / Num. of mol.: 4 / Mutation: E59Q,D222N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: APN2, ETH1, YBL019W, YBL0443 / Production host: Escherichia coli (E. coli)
References: UniProt: P38207, Hydrolases; Acting on ester bonds

-
DNA chain , 2 types, 4 molecules EFGH

#2: DNA chain DNA (5'-D(*TP*CP*CP*GP*AP*AP*AP*TP*(PST)P*(PST)P*(SC)P*(GS)P*(GS))-3')


Mass: 4046.927 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*CP*CP*GP*AP*AP*AP*TP*TP*(PST)P*(SC)P*(GS)P*(GS)P*(AS))-3')


Mass: 4055.940 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

-
Non-polymers , 6 types, 107 molecules

#4: Chemical ChemComp-TAR / D(-)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O6
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O6
#7: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#8: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.48 Å3/Da / Density % sol: 50.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2M sodium citrate, 20% PEG 3350

-
Data collection

DiffractionMean temperature: 105 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Jul 24, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.73→36.97 Å / Num. obs: 51375 / % possible obs: 96.8 % / Redundancy: 3.3 % / Biso Wilson estimate: 67.86 Å2 / Rrim(I) all: 0.085 / Net I/σ(I): 18.4
Reflection shellResolution: 2.73→2.83 Å / Mean I/σ(I) obs: 1.44 / Num. unique obs: 4598 / Rrim(I) all: 0.891

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3G0R

3g0r


Resolution: 2.73→36.97 Å / SU ML: 0.333 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.917
Stereochemistry target values: GEOSTD + MONOMER LIBRARY + CDL V1.2
RfactorNum. reflection% reflection
Rfree0.228 1894 3.69 %
Rwork0.2 --
obs0.201 51347 95.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 101.5 Å2
Refinement stepCycle: LAST / Resolution: 2.73→36.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11597 1036 58 100 12791
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00413055
X-RAY DIFFRACTIONf_angle_d0.6117862
X-RAY DIFFRACTIONf_dihedral_angle_d12.9044734
X-RAY DIFFRACTIONf_chiral_restr0.0472014
X-RAY DIFFRACTIONf_plane_restr0.0042140
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.73-2.80.31791120.28032989X-RAY DIFFRACTION81
2.8-2.870.28541380.26353607X-RAY DIFFRACTION98
2.87-2.960.32351390.25773584X-RAY DIFFRACTION98
2.96-3.050.2791410.24553574X-RAY DIFFRACTION98
3.05-3.160.26841430.25323640X-RAY DIFFRACTION98
3.16-3.290.27121360.21983569X-RAY DIFFRACTION97
3.29-3.440.21891320.21093572X-RAY DIFFRACTION97
3.44-3.620.22531420.20253597X-RAY DIFFRACTION97
3.62-3.840.2571310.19773599X-RAY DIFFRACTION97
3.84-4.140.22651380.18563560X-RAY DIFFRACTION97
4.14-4.560.22221320.17583564X-RAY DIFFRACTION96
4.56-5.210.19651390.1763555X-RAY DIFFRACTION96
5.21-6.560.22491350.20263544X-RAY DIFFRACTION95
6.56-36.970.19471360.18263499X-RAY DIFFRACTION92
Refinement TLS params.Method: refined / Origin x: 5.1379 Å / Origin y: 20.3876 Å / Origin z: 32.6817 Å
111213212223313233
T0.5193 Å20.0399 Å2-0.0076 Å2-0.6846 Å2-0.0636 Å2--0.6381 Å2
L0.5839 °20.0274 °2-0.1047 °2-0.2225 °20.0158 °2--0.3844 °2
S0.0023 Å °-0.5048 Å °0.0482 Å °0.0926 Å °0.012 Å °-0.0062 Å °-0.0181 Å °0.199 Å °-0.0072 Å °
Refinement TLS groupSelection details: ALL

+
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