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- PDB-3g2c: Mth0212 in complex with a short ssDNA (CGTA) -

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Basic information

Entry
Database: PDB / ID: 3g2c
TitleMth0212 in complex with a short ssDNA (CGTA)
Components
  • 5'-D(P*CP*GP*TP*A)-3'
  • Exodeoxyribonuclease
KeywordsHYDROLASE/DNA / protein-DNA complex / single-stranded DNA / flipped nucleotide / PO4 / Mg2+ / 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 / molecular replacement / Resolution: 2.3 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 31, 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 / 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 / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_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_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
I: 5'-D(P*CP*GP*TP*A)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,03015
Polymers64,0523
Non-polymers97812
Water3,027168
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.325, 80.325, 79.611
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32

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Components

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Protein / DNA chain , 2 types, 3 molecules ABI

#1: Protein Exodeoxyribonuclease / Mth0212


Mass: 31430.650 Da / Num. of mol.: 2 / Mutation: T2A
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 (WT) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: O26314, exodeoxyribonuclease III
#2: DNA chain 5'-D(P*CP*GP*TP*A)-3'


Mass: 1190.830 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Non-polymers , 4 types, 180 molecules

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


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 168 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsIN THIS ENTRY, THE FOLLOWING DNAS WERE PREPARED. THE ONE CONSISTS OF CGTA(UPS)TACG AND THE OTHER ...IN THIS ENTRY, THE FOLLOWING DNAS WERE PREPARED. THE ONE CONSISTS OF CGTA(UPS)TACG AND THE OTHER CGTATACG THAT WERE CONSTRUCTED TOGETHER. THEY SLIGHTLY DIFFER IN SEQUENCE, BUT THE 4 NUCLEOTIDE LONG SEQUENCE INCLUDED IN THE COORDINATES IS COMPRISED BY BOTH. THUS, DUE TO LACK OF ELECTRON DENSITY OF THE REMAINING 4 OR 5 RESIDUES OF THE DNA STRAND, THE DEPOSITORS CAN NOT UNAMBIGUOUSLY DISTINGUISH FROM WHICH OF THE TWO DNA SEQUENCES THEY ACTUALLY DERIVE. FOR CLARITY, THEY JUST ASSUMED THEM TO DERIVE FROM ONE KIND OF DNA AND THE OTHER TO HAVE BEEN DEGRADED.

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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: 2.31 Å3/Da / Density % sol: 46.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: reservoir: 25% MPD, 100mM KHEPES pH 7.0; complex 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
6KHEPES12
7H2O12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.815 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: 0.815 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 25521 / % possible obs: 99.8 % / Redundancy: 5.5 % / Biso Wilson estimate: 44.8 Å2 / Rsym value: 0.085 / Net I/σ(I): 17.1
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 4.1 / Rsym value: 0.347 / % possible all: 99.3

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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
MAR345data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3FZI

3fzi


Resolution: 2.3→28.27 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.906 / WRfactor Rfree: 0.274 / WRfactor Rwork: 0.209 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.787 / SU B: 8.348 / SU ML: 0.206 / SU R Cruickshank DPI: 0.422 / SU Rfree: 0.268 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.422 / ESU R Free: 0.268 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; the coordinates of Thr 210 and Arg 211 of chain A are connected via a peptide bond which deviates significantly from both cis and trans ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; the coordinates of Thr 210 and Arg 211 of chain A are connected via a peptide bond which deviates significantly from both cis and trans conformation.; the coordinates representing the Arg 15 of chain A and Thr 210 of chain B have unexpected configuration of the chiral center. They should not be changed.
RfactorNum. reflection% reflectionSelection details
Rfree0.263 1295 5.1 %RANDOM
Rwork0.204 ---
obs0.207 25486 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 83.95 Å2 / Biso mean: 38.834 Å2 / Biso min: 14.99 Å2
Baniso -1Baniso -2Baniso -3
1--0.9 Å2-0.45 Å20 Å2
2---0.9 Å20 Å2
3---1.35 Å2
Refinement stepCycle: LAST / Resolution: 2.3→28.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4273 83 59 168 4583
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0224532
X-RAY DIFFRACTIONr_angle_refined_deg1.5561.9756119
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6065512
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.32722.75240
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.03815763
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1981546
X-RAY DIFFRACTIONr_chiral_restr0.1140.2608
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023481
X-RAY DIFFRACTIONr_nbd_refined0.2030.22074
X-RAY DIFFRACTIONr_nbtor_refined0.3140.22908
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.2305
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1560.235
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2170.214
X-RAY DIFFRACTIONr_mcbond_it0.8041.52620
X-RAY DIFFRACTIONr_mcangle_it1.41424107
X-RAY DIFFRACTIONr_scbond_it1.6932231
X-RAY DIFFRACTIONr_scangle_it2.6984.52011
LS refinement shellResolution: 2.299→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 101 -
Rwork0.258 1794 -
all-1895 -
obs--98.34 %

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