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- PDB-3g00: Mth0212 in complex with a 9bp blunt end dsDNA at 1.7 Angstrom -

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Basic information

Entry
Database: PDB / ID: 3g00
TitleMth0212 in complex with a 9bp blunt end dsDNA at 1.7 Angstrom
Components
  • 5'-D(*CP*GP*TP*AP*TP*TP*AP*CP*G)-3'
  • 5'-D(*CP*GP*TP*AP*UP*TP*AP*CP*G)-3'
  • Exodeoxyribonuclease
KeywordsHYDROLASE/DNA / protein-DNA complex / double-strand specific 3'-5' exonuclease / AP endonuclease / 2'-deoxyuridine 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 uridine endonuclease
Similarity search - Component
Biological speciesMethanothermobacter thermautotrophicus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 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
DepositionJan 27, 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, 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_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_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
H: 5'-D(*CP*GP*TP*AP*TP*TP*AP*CP*G)-3'
I: 5'-D(*CP*GP*TP*AP*UP*TP*AP*CP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,19913
Polymers68,3074
Non-polymers8939
Water11,872659
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6730 Å2
ΔGint-69 kcal/mol
Surface area22960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.966, 79.510, 87.750
Angle α, β, γ (deg.)90.000, 97.760, 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: T2A, D151N
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, 2 molecules HI

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


Mass: 2730.810 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain 5'-D(*CP*GP*TP*AP*UP*TP*AP*CP*G)-3'


Mass: 2716.784 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Non-polymers , 4 types, 668 molecules

#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 659 / 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: 2.48 Å3/Da / Density % sol: 50.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: reservoir: 30% MPD, 40mM MgCl2, 50mM KH2PO4/K2HPO4 pH 7.0; protein solution: 50mM KCl, 10mM KH2PO4/K2HPO4 pH 7.0, 1mM MgCl2, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1KCl11
2KH2PO4/K2HPO411
3MgCl211
4H2O11
5MPD12
6MgCl212
7KH2PO4/K2HPO412
8H2O12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91838 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 13, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91838 Å / Relative weight: 1
ReflectionResolution: 1.74→17 Å / Num. obs: 65383 / % possible obs: 94.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 27.283 Å2 / Rmerge(I) obs: 0.033
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.74-1.80.2683.2166089345172
1.8-1.90.194.63416117080193.8
1.9-20.1286.62988114315197.2
2-2.50.06311.98906742239197.7
2.5-30.03221.44012418827198.4
3-40.02132.53165915034198.9
4-60.01937.6163337745199.2
6-170.01738.366703124199.3

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACT3.006data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3FZI

3fzi


Resolution: 1.74→17 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.94 / WRfactor Rfree: 0.215 / WRfactor Rwork: 0.166 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.868 / SU B: 2.422 / SU ML: 0.079 / SU R Cruickshank DPI: 0.11 / SU Rfree: 0.115 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.11 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.217 3311 5.1 %RANDOM
Rwork0.167 ---
obs0.17 61959 95.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 96.2 Å2 / Biso mean: 24.824 Å2 / Biso min: 8.54 Å2
Baniso -1Baniso -2Baniso -3
1-1.22 Å20 Å2-1.26 Å2
2---2.02 Å20 Å2
3---0.45 Å2
Refinement stepCycle: LAST / Resolution: 1.74→17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4273 361 54 659 5347
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0224907
X-RAY DIFFRACTIONr_angle_refined_deg1.5532.0486701
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2945528
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.04622.735245
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.31615783
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7961548
X-RAY DIFFRACTIONr_chiral_restr0.1120.2673
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023688
X-RAY DIFFRACTIONr_nbd_refined0.1940.22317
X-RAY DIFFRACTIONr_nbtor_refined0.3120.23256
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.2566
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1630.229
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1690.219
X-RAY DIFFRACTIONr_mcbond_it0.941.52668
X-RAY DIFFRACTIONr_mcangle_it1.47424171
X-RAY DIFFRACTIONr_scbond_it2.06232697
X-RAY DIFFRACTIONr_scangle_it2.9914.52524
LS refinement shellResolution: 1.74→1.785 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 184 -
Rwork0.242 3358 -
all-3542 -
obs--71.76 %

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