[English] 日本語
Yorodumi
- PDB-3s6i: Schizosaccaromyces pombe 3-methyladenine DNA glycosylase (Mag1) i... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3s6i
TitleSchizosaccaromyces pombe 3-methyladenine DNA glycosylase (Mag1) in complex with abasic-DNA.
Components
  • (5'-D(*AP*AP*GP*AP*CP*TP*TP*GP*GP*AP*C)-3')
  • (5'-D(*TP*GP*TP*CP*CP*AP*(3DR)P*GP*TP*CP*T)-3')
  • DNA-3-methyladenine glycosylase 1
KeywordsHYDROLASE/DNA / DNA Glycosylase / DNA repair / Helix-hairpin-Helix (HhH) / abasic site / tetrahydrofuran (THF) / HYDROLASE-DNA complex
Function / homology
Function and homology information


DNA-1,N6-ethenoadenine N-glycosylase activity / alkylated DNA binding / alkylbase DNA N-glycosylase activity / DNA-7-methyladenine glycosylase activity / DNA-3-methylguanine glycosylase activity / DNA-3-methyladenine glycosylase II / DNA-7-methylguanine glycosylase activity / DNA-3-methyladenine glycosylase activity / base-excision repair, AP site formation / DNA alkylation repair ...DNA-1,N6-ethenoadenine N-glycosylase activity / alkylated DNA binding / alkylbase DNA N-glycosylase activity / DNA-7-methyladenine glycosylase activity / DNA-3-methylguanine glycosylase activity / DNA-3-methyladenine glycosylase II / DNA-7-methylguanine glycosylase activity / DNA-3-methyladenine glycosylase activity / base-excision repair, AP site formation / DNA alkylation repair / protein-DNA complex / damaged DNA binding / nucleus
Similarity search - Function
Endonuclease Iii, domain 2 - #40 / Alkylbase DNA glycosidase, conserved site / Alkylbase DNA glycosidases alkA family signature. / : / Endonuclease Iii, domain 2 / Hypothetical protein; domain 2 / HhH-GPD superfamily base excision DNA repair protein / HhH-GPD domain / endonuclease III / Endonuclease III; domain 1 ...Endonuclease Iii, domain 2 - #40 / Alkylbase DNA glycosidase, conserved site / Alkylbase DNA glycosidases alkA family signature. / : / Endonuclease Iii, domain 2 / Hypothetical protein; domain 2 / HhH-GPD superfamily base excision DNA repair protein / HhH-GPD domain / endonuclease III / Endonuclease III; domain 1 / DNA glycosylase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA-3-methyladenine glycosylase 1
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.28 Å
AuthorsAdhikary, S. / Eichman, B.F.
CitationJournal: Embo Rep. / Year: 2011
Title: Analysis of substrate specificity of Schizosaccharomyces pombe Mag1 alkylpurine DNA glycosylase.
Authors: Adhikary, S. / Eichman, B.F.
History
DepositionMay 25, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2011Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: DNA-3-methyladenine glycosylase 1
B: (5'-D(*TP*GP*TP*CP*CP*AP*(3DR)P*GP*TP*CP*T)-3')
C: (5'-D(*AP*AP*GP*AP*CP*TP*TP*GP*GP*AP*C)-3')
D: DNA-3-methyladenine glycosylase 1
E: (5'-D(*TP*GP*TP*CP*CP*AP*(3DR)P*GP*TP*CP*T)-3')
F: (5'-D(*AP*AP*GP*AP*CP*TP*TP*GP*GP*AP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,0408
Polymers65,9946
Non-polymers462
Water2,018112
1
A: DNA-3-methyladenine glycosylase 1
B: (5'-D(*TP*GP*TP*CP*CP*AP*(3DR)P*GP*TP*CP*T)-3')
C: (5'-D(*AP*AP*GP*AP*CP*TP*TP*GP*GP*AP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0204
Polymers32,9973
Non-polymers231
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3580 Å2
ΔGint-29 kcal/mol
Surface area12380 Å2
MethodPISA
2
D: DNA-3-methyladenine glycosylase 1
E: (5'-D(*TP*GP*TP*CP*CP*AP*(3DR)P*GP*TP*CP*T)-3')
F: (5'-D(*AP*AP*GP*AP*CP*TP*TP*GP*GP*AP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0204
Polymers32,9973
Non-polymers231
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3370 Å2
ΔGint-31 kcal/mol
Surface area12740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.317, 112.298, 61.113
Angle α, β, γ (deg.)90.00, 99.55, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein DNA-3-methyladenine glycosylase 1 / 3-methyladenine DNA glycosidase 1 / 3MEA DNA glycosylase 1


Mass: 26423.529 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Strain: ATCC 38366 / 972 / Gene: mag1, SPAPB24D3.04c / Plasmid: pBG100 / Production host: Escherichia coli (E. coli) / Strain (production host): C41
References: UniProt: Q92383, DNA-3-methyladenine glycosylase II
#2: DNA chain (5'-D(*TP*GP*TP*CP*CP*AP*(3DR)P*GP*TP*CP*T)-3')


Mass: 3191.073 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Synthetic construct
#3: DNA chain (5'-D(*AP*AP*GP*AP*CP*TP*TP*GP*GP*AP*C)-3')


Mass: 3382.236 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Synthetic construct
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 2.79 Å3/Da / Density % sol: 55.84 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M MES (pH 6.5), 20% (w/v) PEG 8K and 2.4% (v/v) glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 294K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11101
21101
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 22-BM10.9792
SYNCHROTRONAPS 21-ID-D20.97872
Detector
TypeIDDetectorDate
MARMOSAIC 225 mm CCD1CCDFeb 16, 2009
MARMOSAIC 300 mm CCD2CCDFeb 17, 2009
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si(111)SINGLE WAVELENGTHMx-ray1
2Si(111)SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97921
20.978721
ReflectionResolution: 2.28→29.1 Å / Num. all: 32231 / Num. obs: 32231 / % possible obs: 99.6 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Biso Wilson estimate: 40.8 Å2 / Rsym value: 0.109 / Net I/σ(I): 11.5
Reflection shellResolution: 2.28→2.38 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 2.5 / Num. unique all: 3176 / Rsym value: 0.404 / % possible all: 98.1

-
Processing

Software
NameVersionClassification
HKL-2000data collection
SHARPphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.28→29.1 Å / SU ML: 0.64 / σ(F): 1.35 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2254 1631 5.07 %random
Rwork0.1849 ---
all0.2362 32199 --
obs0.1869 32188 97.29 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.382 Å2 / ksol: 0.345 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--7.1752 Å2-0 Å21.0957 Å2
2---2.3552 Å2-0 Å2
3---9.5304 Å2
Refinement stepCycle: LAST / Resolution: 2.28→29.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3184 845 2 112 4143
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084196
X-RAY DIFFRACTIONf_angle_d1.1855864
X-RAY DIFFRACTIONf_dihedral_angle_d21.871577
X-RAY DIFFRACTIONf_chiral_restr0.068663
X-RAY DIFFRACTIONf_plane_restr0.005605
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.277-2.34390.2383860.21761871X-RAY DIFFRACTION71
2.3439-2.41960.26251480.20392544X-RAY DIFFRACTION99
2.4196-2.5060.27541470.19792601X-RAY DIFFRACTION100
2.506-2.60630.23461410.2062602X-RAY DIFFRACTION100
2.6063-2.72480.26231450.20842604X-RAY DIFFRACTION100
2.7248-2.86830.24561480.21022610X-RAY DIFFRACTION100
2.8683-3.04790.26991360.19812616X-RAY DIFFRACTION100
3.0479-3.28290.20851270.19112625X-RAY DIFFRACTION100
3.2829-3.61270.24291310.16712623X-RAY DIFFRACTION100
3.6127-4.13420.18241390.15372626X-RAY DIFFRACTION100
4.1342-5.20380.17641320.1462628X-RAY DIFFRACTION100
5.2038-29.10560.20091510.16812607X-RAY DIFFRACTION98
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)
11.8103-1.09220.47042.3258-0.61990.68310.08570.3957-0.05810.006-0.0918-0.28020.09540.02270.0080.14730.02720.00310.20130.03970.2239-23.092-10.509-6.6375
20.8415-0.91990.33553.166-0.9570.976-0.08870.1582-0.2275-0.04090.30960.5915-0.0383-0.2743-0.19560.08440.01830.0330.19160.08720.2006-40.3994-8.782-4.9127
30.9105-0.5468-0.22040.9315-0.38160.5959-0.0695-0.05080.81830.1427-0.1053-0.8629-0.21740.39860.17890.10320.0098-0.10160.23620.03180.4654-16.0715-2.3271-1.2033
41.2008-1.13871.74062.93760.11962.21530.24820.11610.4417-0.5739-0.42010.2555-0.3077-0.55370.2010.23440.0438-0.07350.2977-0.01430.3117-40.6524-34.063314.6793
51.09750.1053-0.51021.73190.75981.3108-0.0811-0.03790.0728-0.06040.1157-0.178-0.03330.2315-0.06660.0635-0.0026-0.02240.176-0.04220.1046-15.4127-36.362329.3272
60.823-0.40290.63420.360.19440.8646-0.0324-0.1564-0.1139-0.0471-0.05490.4424-0.0183-0.39170.09510.1147-0.0018-0.03420.229-0.00930.2903-39.18-38.441225.9458
70.7236-0.08770.85674.8545-2.71433.1794-0.06830.15730.02951.3938-0.4766-0.5662-1.12120.27860.31730.38190.1099-0.08160.13620.04220.1137-28.526-11.65114.5949
83.073-0.86270.71683.3019-3.24110.4207-0.656-1.47750.03012.06310.2566-0.2862-0.82430.39930.35670.77230.1658-0.23220.587-0.01320.3744-29.3632-12.246914.7463
91.4719-2.1411-1.56375.61792.05611.1332-0.21930.1119-0.17851.2822-0.14670.99150.2697-0.11430.29070.37140.05310.16310.1294-0.04010.218-30.1511-32.194744.5575
100.1050.8552-0.30191.5792-0.71871.7698-0.1492-0.36220.15240.59050.12880.86750.0306-0.38840.10410.31410.17830.21850.3623-0.11730.4431-28.7828-29.866644.7184
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 17:74)
2X-RAY DIFFRACTION2(chain A and resid 75:163)
3X-RAY DIFFRACTION3(chain A and resid 164:220)
4X-RAY DIFFRACTION4(chain D and resid 17:42)
5X-RAY DIFFRACTION5(chain D and resid 43:164)
6X-RAY DIFFRACTION6(chain D and resid 165:219)
7X-RAY DIFFRACTION7chain B
8X-RAY DIFFRACTION8chain C
9X-RAY DIFFRACTION9chain E
10X-RAY DIFFRACTION10chain F

+
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