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- PDB-3g0r: Complex of Mth0212 and an 8bp dsDNA with distorted ends -

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Basic information

Entry
Database: PDB / ID: 3g0r
TitleComplex of Mth0212 and an 8bp dsDNA with distorted ends
Components
  • 5'-D(*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*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
DNA / DNA (> 10) / DNA uridine endonuclease
Similarity search - Component
Biological speciesMethanothermobacter thermautotrophicus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 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 28, 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
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 / diffrn_source / pdbx_initial_refinement_model / struct_conn / 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 / _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_dist_value / _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_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
G: 5'-D(*GP*CP*TP*GP*CP*GP*CP*AP*GP*GP*GP*CP*G)-3'
K: 5'-D(*CP*CP*CP*TP*GP*UP*GP*CP*AP*GP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,92321
Polymers70,1894
Non-polymers1,73417
Water5,495305
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9700 Å2
ΔGint-42 kcal/mol
Surface area22850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.751, 80.760, 105.211
Angle α, β, γ (deg.)90.00, 94.03, 90.00
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 GK

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


Mass: 4033.609 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain 5'-D(*CP*CP*CP*TP*GP*UP*GP*CP*AP*GP*C)-3'


Mass: 3296.135 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Non-polymers , 4 types, 322 molecules

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


Mass: 92.094 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 305 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsTHE 2ND DC IN CHAIN K STANDS FOR THE MODIFIED NUCLEOTIDE 5- BROMO-2'DC. SINCE THERE WAS NO HINT FOR ...THE 2ND DC IN CHAIN K STANDS FOR THE MODIFIED NUCLEOTIDE 5- BROMO-2'DC. SINCE THERE WAS NO HINT FOR A BROMO ATOM AT THE APPROPRIATE POSITION IN THE ELECTRON DENSITY, THE DEPOSITOR REFINED THE RESIDUE JUST AS DC. REASONS FOR THE ABSENCE MIGHT EITHER BE AN INEFFICIENT INCORPORATION OF THE MODIFIED NUCLEOTIDES DURING DNA SYNTHESIS, A BREAK OF THE BOND BETWEEN THE APPROPRIATE C5 RING OF RESIDUE 2 IN CHAIN G AND THE BROMO ATOM CAUSED BY HEATING OR LIGHT DURING THE ANNEALING PROCEDURE OR CRYSTALLIZATION. ANOTHER EXPLANATION FOR THE ABSENCE OF THE BROMO LABEL MIGHT BE RADIATION DAMAGE DURING DATA COLLECTION.

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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: 2.7 Å3/Da / Density % sol: 54.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: reservoir: 189mM KCl, 9.5mM MgCl2, 4.7% (w/v) PEG 8000, 47mM MES/NaOH pH 5.6, 2.1% 1,4-butanediol, 2mM DTT; protein solution: 234mM NaCl, 7mM KHEPES pH 7.6, 1.83mM MgCl2, 2.7mM DTT, VAPOR ...Details: reservoir: 189mM KCl, 9.5mM MgCl2, 4.7% (w/v) PEG 8000, 47mM MES/NaOH pH 5.6, 2.1% 1,4-butanediol, 2mM DTT; protein solution: 234mM NaCl, 7mM KHEPES pH 7.6, 1.83mM MgCl2, 2.7mM DTT, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1NaCl11
2KHEPES11
3MgCl211
4DTT11
5H2O11
6KCL12
7MgCl212
8PEG 800012
9MES/NaOH12
101,4-butanediol12
11DTT12
12H2O12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 0.97623 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 5, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97623 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 27308 / % possible obs: 92.8 % / Redundancy: 4.7 % / Rsym value: 0.061 / Net I/σ(I): 22.7
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 5.2 / Rsym value: 0.191 / % possible all: 72.3

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Phasing

PhasingMethod: molecular replacement

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Processing

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

3fzi


Resolution: 2.4→44.64 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.906 / WRfactor Rfree: 0.226 / WRfactor Rwork: 0.171 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.824 / SU B: 7.338 / SU ML: 0.174 / SU R Cruickshank DPI: 0.427 / SU Rfree: 0.271 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.427 / ESU R Free: 0.27 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24286 1391 5.1 %RANDOM
Rwork0.17782 ---
obs0.1811 27293 92.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 71.56 Å2 / Biso mean: 27.829 Å2 / Biso min: 4.11 Å2
Baniso -1Baniso -2Baniso -3
1--0.7 Å20 Å21.12 Å2
2---0.83 Å20 Å2
3---1.69 Å2
Refinement stepCycle: LAST / Resolution: 2.4→44.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4252 423 113 305 5093
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0224936
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5862.0736706
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2015507
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.67522.75240
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.10215758
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.711546
X-RAY DIFFRACTIONr_chiral_restr0.0990.2667
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023641
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2090.22358
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3090.23189
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.2374
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2240.246
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1920.216
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6981.52529
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.32824078
X-RAY DIFFRACTIONr_scbond_it1.78832592
X-RAY DIFFRACTIONr_scangle_it2.844.52628
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.399→2.461 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 68 -
Rwork0.197 1482 -
obs--70.68 %

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