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- PDB-3ga6: Mth0212 in complex with two DNA helices -

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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


double-stranded DNA 3'-5' DNA exonuclease activity / exodeoxyribonuclease III / phosphoric diester hydrolase activity / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / base-excision repair / endonuclease activity / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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Components

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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

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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

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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

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Experimental details

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Experiment

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

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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

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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

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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

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