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- PDB-3g38: The catalytically inactive mutant Mth0212 (D151N) in complex with... -

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Basic information

Entry
Database: PDB / ID: 3g38
TitleThe catalytically inactive mutant Mth0212 (D151N) in complex with an 8 bp dsDNA
Components
  • 5'-D(*CP*CP*TP*GP*UP*GP*CP*GP*AP*T)-3'
  • 5'-D(*CP*GP*CP*GP*CP*AP*GP*GP*C)-3'
  • Exodeoxyribonuclease
KeywordsHYDROLASE/DNA / protein-DNA complex / 3'- phosphate moiety bound / HYDROLASE-DNA COMPLEX
Function / homology
Function and homology information


exodeoxyribonuclease III / double-stranded DNA 3'-5' DNA exonuclease activity / 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 uridine endonuclease
Similarity search - Component
Biological speciesMethanothermobacter thermautotrophicus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.04 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 2, 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 / 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

Downloads & links

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Assembly

Deposited unit
A: Exodeoxyribonuclease
G: 5'-D(*CP*CP*TP*GP*UP*GP*CP*GP*AP*T)-3'
K: 5'-D(*CP*GP*CP*GP*CP*AP*GP*GP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7469
Polymers37,1933
Non-polymers5536
Water86548
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2510 Å2
ΔGint-16 kcal/mol
Surface area13180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.960, 107.150, 44.270
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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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
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: DNA chain 5'-D(*CP*CP*TP*GP*UP*GP*CP*GP*AP*T)-3'


Mass: 3021.964 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain 5'-D(*CP*GP*CP*GP*CP*AP*GP*GP*C)-3'


Mass: 2741.800 Da / Num. of mol.: 1 / Source method: obtained synthetically
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 2.55 Å3/Da / Density % sol: 51.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: reservoir: 5% (w/v) PEG 4000, 50mM KCl, 100mM MES pH 5.6, 10mM MgCl2; complex solution: 230mM 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 400012
7KCl12
8MES12
9MgCl212
10H2O12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8015 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: May 17, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8015 Å / Relative weight: 1
ReflectionResolution: 2.74→36.424 Å / Num. obs: 10553 / % possible obs: 100 % / Redundancy: 7.6 % / Biso Wilson estimate: 54.9 Å2 / Rmerge(I) obs: 0.117 / Rsym value: 0.117 / Net I/σ(I): 5.881 / Num. measured all: 80599
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.74-2.897.80.4711.61170814970.471100
2.89-3.067.80.3272.31114514360.327100
3.06-3.277.80.2063.61048013430.206100
3.27-3.547.80.1365.3968012490.136100
3.54-3.877.70.1056.8894811660.105100
3.87-4.337.70.0818.1817110640.081100
4.33-57.60.0689.571919480.068100
5-6.137.50.0768.560938170.076100
6.13-8.667.30.0788.546476400.078100
8.66-37.456.50.0510.425363930.0598.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.25data scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
MAR345data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDN ENTRY 3FZI

3fzi


Resolution: 3.04→34.13 Å / Cor.coef. Fo:Fc: 0.878 / Cor.coef. Fo:Fc free: 0.779 / WRfactor Rfree: 0.303 / WRfactor Rwork: 0.235 / Occupancy max: 1 / Occupancy min: 0.99 / FOM work R set: 0.711 / SU B: 30.97 / SU ML: 0.55 / SU Rfree: 0.594 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.594 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; The DNA conformation significantly deviates from ideal geometry due to the binding to the protein molecule
RfactorNum. reflection% reflectionSelection details
Rfree0.328 361 4.6 %RANDOM
Rwork0.256 ---
obs0.259 7784 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 93.28 Å2 / Biso mean: 37.113 Å2 / Biso min: 18.88 Å2
Baniso -1Baniso -2Baniso -3
1--1.41 Å20 Å20 Å2
2--8.51 Å20 Å2
3----7.1 Å2
Refinement stepCycle: LAST / Resolution: 3.04→34.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2143 326 36 48 2553
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0222594
X-RAY DIFFRACTIONr_angle_refined_deg1.3812.1153553
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.075256
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.89322.75120
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.36515382
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1941523
X-RAY DIFFRACTIONr_chiral_restr0.0840.2359
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021889
X-RAY DIFFRACTIONr_nbd_refined0.2330.21439
X-RAY DIFFRACTIONr_nbtor_refined0.3160.21672
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.2135
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1970.225
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2660.25
LS refinement shellResolution: 3.04→3.119 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 27 -
Rwork0.277 519 -
all-546 -
obs--100 %

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