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- PDB-3g8v: The rationally designed catalytically inactive mutant Mth0212(D151N) -

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Basic information

Entry
Database: PDB / ID: 3g8v
TitleThe rationally designed catalytically inactive mutant Mth0212(D151N)
ComponentsExodeoxyribonuclease
KeywordsHYDROLASE / alpha/beta-sandwich / double-strand specific 3'-5' exonuclease / AP endonuclease / 2'-desoxyuridine endonuclease / rationally designed catalytically inactive mutant
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 uridine endonuclease
Similarity search - Component
Biological speciesMethanothermobacter thermautotrophicus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / 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
DepositionFeb 12, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
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 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _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

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Assembly

Deposited unit
A: Exodeoxyribonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9005
Polymers31,4301
Non-polymers4714
Water1,802100
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.310, 60.310, 149.450
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Exodeoxyribonuclease / Mth0212


Mass: 31429.666 Da / Num. of mol.: 1 / Mutation: T2A, D151N
Source method: isolated from a genetically manipulated source
Details: strain used for expression lacks the gene ung coding for a uracil DNA glycosylase
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
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 2.5 Å3/Da / Density % sol: 50.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: reservoir solution: 15 % (w/v) PEG 3350, 15mM sodium cacodylate pH 6.5, 25mM MnCl2; protein solution: 120mM NaCl, 2mM DTT, 8mM HEPES-NaOH pH 7.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.979 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Sep 18, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.4→30.39 Å / Num. obs: 12026 / % possible obs: 99.8 % / Redundancy: 4.1 % / Biso Wilson estimate: 54.7 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 15.7
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.265 / Mean I/σ(I) obs: 4.1 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT3.006data extraction
MAR345data collection
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3FZI

3fzi


Resolution: 2.4→29.56 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.878 / WRfactor Rfree: 0.273 / WRfactor Rwork: 0.216 / Occupancy max: 1 / Occupancy min: 0.99 / FOM work R set: 0.764 / SU B: 9.361 / SU ML: 0.229 / SU R Cruickshank DPI: 0.526 / SU Rfree: 0.304 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.526 / ESU R Free: 0.304 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27996 578 4.8 %RANDOM
Rwork0.2201 ---
obs0.22302 11971 99.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 75.77 Å2 / Biso mean: 39.781 Å2 / Biso min: 22.58 Å2
Baniso -1Baniso -2Baniso -3
1--0.83 Å2-0.41 Å20 Å2
2---0.83 Å20 Å2
3---1.24 Å2
Refinement stepCycle: LAST / Resolution: 2.4→29.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2127 0 31 100 2258
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222212
X-RAY DIFFRACTIONr_angle_refined_deg1.4251.9512972
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9745254
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.05122.75120
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.59415378
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2251523
X-RAY DIFFRACTIONr_chiral_restr0.1070.2293
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021714
X-RAY DIFFRACTIONr_nbd_refined0.1960.21003
X-RAY DIFFRACTIONr_nbtor_refined0.3080.21457
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.2134
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1740.218
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1620.28
X-RAY DIFFRACTIONr_mcbond_it0.7261.51309
X-RAY DIFFRACTIONr_mcangle_it1.24322042
X-RAY DIFFRACTIONr_scbond_it1.40431048
X-RAY DIFFRACTIONr_scangle_it2.1964.5930
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.364 44 -
Rwork0.25 821 -
all-865 -
obs--100 %

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