[English] 日本語
Yorodumi
- PDB-3ga6: Mth0212 in complex with two DNA helices -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3ga6
TitleMth0212 in complex with two DNA helices
Components
  • 5'-D(*GP*CP*CP*CP*TP*GP*UP*GP*CP*AP*GP*C)-3'
  • 5'-D(*GP*CP*TP*GP*CP*GP*CP*AP*GP*GP*GP*C)-3'
  • Exodeoxyribonuclease
KeywordsHYDROLASE/DNA / protein-DNA complex / twin / disorder of DNA / 3'-5' exonuclease / AP endonuclease / 2'-desoxyuridine endonuclease / HYDROLASE-DNA COMPLEX
Function / homology
Function and homology information


exodeoxyribonuclease III / double-stranded DNA 3'-5' DNA exonuclease activity / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / endonuclease activity / DNA repair / DNA binding / metal ion binding
Similarity search - Function
AP endonuclease 1, binding site / AP endonucleases family 1 signature 1. / 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
PHOSPHATE ION / DNA / DNA (> 10) / DNA uridine endonuclease
Similarity search - Component
Biological speciesMethanothermobacter thermautotrophicus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.898 Å
AuthorsLakomek, K. / Dickmanns, A. / Ficner, R.
Citation
Journal: J.Mol.Biol. / Year: 2010
Title: Crystal Structure Analysis of DNA Uridine Endonuclease Mth212 Bound to DNA
Authors: Lakomek, K. / Dickmanns, A. / Ciirdaeva, E. / Schomacher, L. / Ficner, R.
#1: Journal: Nucleic Acids Res. / Year: 2006
Title: The Methanothermobacter thermautotrophicus ExoIII homologue Mth212 is a DNA uridine endonuclease
Authors: Georg, J. / Schomacher, L. / Chong, J.P.J. / Majernik, A.I. / Raabe, M. / Urlaub, H. / Muller, S. / Ciirdaeva, E. / Kramer, W. / Fritz, H.-J.
History
DepositionFeb 16, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 12, 2014Group: Derived calculations
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq / 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_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _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: Exodeoxyribonuclease
B: Exodeoxyribonuclease
F: 5'-D(*GP*CP*TP*GP*CP*GP*CP*AP*GP*GP*GP*C)-3'
G: 5'-D(*GP*CP*CP*CP*TP*GP*UP*GP*CP*AP*GP*C)-3'
H: 5'-D(*GP*CP*TP*GP*CP*GP*CP*AP*GP*GP*GP*C)-3'
D: 5'-D(*GP*CP*CP*CP*TP*GP*UP*GP*CP*AP*GP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,48228
Polymers77,5196
Non-polymers1,96322
Water6,377354
1
A: Exodeoxyribonuclease
F: 5'-D(*GP*CP*TP*GP*CP*GP*CP*AP*GP*GP*GP*C)-3'
D: 5'-D(*GP*CP*CP*CP*TP*GP*UP*GP*CP*AP*GP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,79515
Polymers38,7593
Non-polymers1,03612
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Exodeoxyribonuclease
G: 5'-D(*GP*CP*CP*CP*TP*GP*UP*GP*CP*AP*GP*C)-3'
H: 5'-D(*GP*CP*TP*GP*CP*GP*CP*AP*GP*GP*GP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,68613
Polymers38,7593
Non-polymers92710
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.834, 126.655, 54.826
Angle α, β, γ (deg.)90.000, 93.140, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Exodeoxyribonuclease / Mth0212


Mass: 31429.666 Da / Num. of mol.: 2 / Mutation: T1002/2002A, D1151/2151N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothermobacter thermautotrophicus (archaea)
Strain: Delta H (DSM 1053) / Gene: mth0212, MTH212, MTH_212 / Plasmid: pET_B_001-mth212 (D151N) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: O26314, exodeoxyribonuclease III

-
DNA chain , 2 types, 4 molecules FHGD

#2: DNA chain 5'-D(*GP*CP*TP*GP*CP*GP*CP*AP*GP*GP*GP*C)-3'


Mass: 3704.404 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: DNA chain 5'-D(*GP*CP*CP*CP*TP*GP*UP*GP*CP*AP*GP*C)-3'


Mass: 3625.341 Da / Num. of mol.: 2 / Source method: obtained synthetically

-
Non-polymers , 4 types, 376 molecules

#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 354 / 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: 2.45 Å3/Da / Density % sol: 49.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: reservoir solution: 5% (w/v) PEG 8000, 200mM KCl, 10 mM MgCl2, 50mM MES pH 5.6, 2mM DTT; complex solution: 245mM NaCl, 8mM HEPES-KOH pH 7.6, 2mM MgCl2, 3mM DTT , VAPOR DIFFUSION, SITTING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1NaCl11
2HEPES-KOH11
3MgCl211
4DTT11
5H2O11
6PEG 800012
7KCl12
8MgCl212
9MES12
10DTT12
11H2O12

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.918 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 18, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
Reflection twinOperator: l,-k,h / Fraction: 0.505
ReflectionResolution: 1.898→50 Å / Num. obs: 56272 / % possible obs: 95.8 % / Redundancy: 6.7 % / Biso Wilson estimate: 28 Å2 / Rsym value: 0.075 / Net I/σ(I): 22.2
Reflection shellResolution: 1.898→1.97 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 1.8 / Rsym value: 0.607 / % possible all: 72.2

-
Processing

Software
NameVersionClassificationNB
PHENIXrefinement
PDB_EXTRACT3.006data extraction
MAR345data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3FZI

3fzi


Resolution: 1.898→33.709 Å / Occupancy max: 1 / Occupancy min: 0.37 / FOM work R set: 0.851 / Cross valid method: THROUGHOUT / σ(F): 0.06 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.203 3326 6.32 %in (40) thin shells (using DATAMAN), 6.0 %
Rwork0.155 ---
obs0.158 52596 89.39 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.625 Å2 / ksol: 0.353 e/Å3
Displacement parametersBiso max: 223.5 Å2 / Biso mean: 36.76 Å2 / Biso min: 11.76 Å2
Baniso -1Baniso -2Baniso -3
1--3.515 Å20 Å2-6.494 Å2
2--5.798 Å20 Å2
3----3.82 Å2
Refinement stepCycle: LAST / Resolution: 1.898→33.709 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4249 901 125 354 5629
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085476
X-RAY DIFFRACTIONf_angle_d1.3597543
X-RAY DIFFRACTIONf_chiral_restr0.088760
X-RAY DIFFRACTIONf_plane_restr0.005813
X-RAY DIFFRACTIONf_dihedral_angle_d22.342081
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20 / % reflection obs: 98 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.898-1.9310.287720.27115401612
1.931-1.9660.2381360.2617761912
1.966-2.0040.2461380.23819342072
2.004-2.0450.2861690.23122842453
2.045-2.0890.2841430.22224292572
2.089-2.1380.2561890.2125212710
2.138-2.1910.2381520.20126002752
2.191-2.2510.2331710.19624472618
2.251-2.3170.241500.19525142664
2.317-2.3920.2091770.1925802757
2.392-2.4770.2351340.1925362670
2.477-2.5760.231390.18225812720
2.576-2.6930.2271570.17526262783
2.693-2.8350.1891590.16726582817
2.835-3.0130.2531650.15926702835
3.013-3.2450.1742010.14126792880
3.245-3.5720.1851400.12427812921
3.572-4.0880.171670.11527592926
4.088-5.1470.1551790.09627482927
5.147-33.7140.2012310.16127642995
Refinement TLS params.

S33: -0 Å ° / 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 °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.429-0.3030.53110.4577-0.33020.7251-0.08280.11580.01380.0563-0.009-0.0084-0.05690.13660.0702-0.01580.00620.08370.00240.071223.11858.0566-3.6572
20.78270.250.53530.4720.21090.43680.0626-0.0665-0.05390.01340.0512-0.01570.0039-0.05990.08560.00910.00590.08350.01970.0733-4.9497-8.228222.8991
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

+
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