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- PDB-3g0a: Mth0212 with two bound manganese ions -

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Basic information

Entry
Database: PDB / ID: 3g0a
TitleMth0212 with two bound manganese ions
ComponentsExodeoxyribonuclease
KeywordsHYDROLASE / coordination of two manganese ions / double-strand specific 3'-5' exonuclease / AP endonuclease / 2'-deoxyuridine endonuclease
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 uridine endonuclease
Similarity search - Component
Biological speciesMethanothermobacter thermautotrophicus (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 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 1.2Nov 1, 2017Group: Refinement description / Category: software
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 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7285
Polymers31,4311
Non-polymers2974
Water1,27971
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.381, 56.381, 162.932
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Exodeoxyribonuclease / Mth0212


Mass: 31430.650 Da / Num. of mol.: 1 / Mutation: T2A
Source method: isolated from a genetically manipulated source
Details: lacking the gene "ung"
Source: (gene. exp.) Methanothermobacter thermautotrophicus (archaea)
Strain: Delta H (DSM 1053) / Gene: mth0212, MTH212, MTH_212 / Plasmid: pET_B_001-mth212 (WT) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21_UX / References: UniProt: O26314, exodeoxyribonuclease III
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / 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: 2.38 Å3/Da / Density % sol: 48.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: reservoir solution: 10% (w/v) PEG 20000, 100mM MES-NaOH pH 6.5; protein solution: 600mM NaCl, 20mM HEPES-KOH pH 7.6, 2mM DTT; soaking in 6% (w/v) PEG 20000, 23% (v/v) glycerol, 60mM MES-NaOH ...Details: reservoir solution: 10% (w/v) PEG 20000, 100mM MES-NaOH pH 6.5; protein solution: 600mM NaCl, 20mM HEPES-KOH pH 7.6, 2mM DTT; soaking in 6% (w/v) PEG 20000, 23% (v/v) glycerol, 60mM MES-NaOH pH 6.5, 200mM MnCl2, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 130 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Feb 28, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 8864 / % possible obs: 96.6 % / Redundancy: 6.5 % / Rsym value: 0.095 / Net I/σ(I): 17
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 2.4 % / Rsym value: 0.351

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.2.0019refinement
PDB_EXTRACT3.006data extraction
MAR345data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3FZI

3fzi


Resolution: 2.6→48.83 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.896 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 11.573 / SU ML: 0.245 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.345 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.252 415 4.7 %RANDOM
Rwork0.19 ---
obs0.193 8440 98.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 75.26 Å2 / Biso mean: 32.202 Å2 / Biso min: 9.09 Å2
Baniso -1Baniso -2Baniso -3
1-1.95 Å20.97 Å20 Å2
2--1.95 Å20 Å2
3----2.92 Å2
Refinement stepCycle: LAST / Resolution: 2.6→48.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2147 0 13 71 2231
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222221
X-RAY DIFFRACTIONr_angle_refined_deg1.3551.9472994
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.595257
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.37322.81121
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.94615388
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0111523
X-RAY DIFFRACTIONr_chiral_restr0.0990.2298
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021730
X-RAY DIFFRACTIONr_nbd_refined0.1990.2994
X-RAY DIFFRACTIONr_nbtor_refined0.3150.21468
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.2119
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2210.225
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1130.210
X-RAY DIFFRACTIONr_mcbond_it0.5731.51307
X-RAY DIFFRACTIONr_mcangle_it1.03122065
X-RAY DIFFRACTIONr_scbond_it1.12131044
X-RAY DIFFRACTIONr_scangle_it1.8684.5928
LS refinement shellResolution: 2.603→2.67 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.422 31 -
Rwork0.301 580 -
all-611 -
obs--90.38 %

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