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- PDB-3g4t: Mth0212 (WT) in complex with a 7bp dsDNA -

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Basic information

Entry
Database: PDB / ID: 3g4t
TitleMth0212 (WT) in complex with a 7bp dsDNA
Components
  • 5'-D(*CP*G*TP*AP*CP*TP*AP*CP*G)-3'
  • 5'-D(*CP*GP*TP*AP*(UPS)P*TP*AP*CP*G)-3'
  • Exodeoxyribonuclease
KeywordsHYDROLASE/DNA / protein-DNA complex / double-stranded DNA / inorganic phosphate / 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: 2.64 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 4, 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 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / 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_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_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.pdbx_leaving_atom_flag / _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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_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
H: 5'-D(*CP*GP*TP*AP*(UPS)P*TP*AP*CP*G)-3'
I: 5'-D(*CP*G*TP*AP*CP*TP*AP*CP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,6439
Polymers68,3104
Non-polymers3345
Water28816
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5150 Å2
ΔGint-49 kcal/mol
Surface area22480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.764, 79.600, 99.409
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B
13A
23B
14A
24B
15A
25B
16A
26B
17A
27B
18A
28B

NCS domain segments:

Component-ID: 1 / Refine code: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ILEILEPHEPHEAA6 - 266 - 26
21ILEILEPHEPHEBB6 - 266 - 26
12GLUGLUPROPROAA28 - 4728 - 47
22GLUGLUPROPROBB28 - 4728 - 47
13VALVALGLUGLUAA53 - 11953 - 119
23VALVALGLUGLUBB53 - 11953 - 119
14ARGARGASNASNAA121 - 137121 - 137
24ARGARGASNASNBB121 - 137121 - 137
15GLUGLUGLYGLYAA139 - 143139 - 143
25GLUGLUGLYGLYBB139 - 143139 - 143
16ASNASNALAALAAA145 - 162145 - 162
26ASNASNALAALABB145 - 162145 - 162
17PROPROLEULEUAA164 - 240164 - 240
27PROPROLEULEUBB164 - 240164 - 240
18METMETILEILEAA244 - 255244 - 255
28METMETILEILEBB244 - 255244 - 255

NCS ensembles :
ID
1
2
3
4
5
6
7
8

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Components

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Protein , 1 types, 2 molecules AB

#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

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DNA chain , 2 types, 2 molecules HI

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


Mass: 2732.849 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain 5'-D(*CP*G*TP*AP*CP*TP*AP*CP*G)-3'


Mass: 2715.799 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Non-polymers , 3 types, 21 molecules

#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsTHE 3'-END OF BOTH CHAIN I IS BOUND TO ROX 5/6 NHS MIXTURE (FLUORESCENCE DYE), WHICH IS NOT SHOWN ...THE 3'-END OF BOTH CHAIN I IS BOUND TO ROX 5/6 NHS MIXTURE (FLUORESCENCE DYE), WHICH IS NOT SHOWN IN THIS ENTRY.

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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: 2.92 Å3/Da / Density % sol: 57.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: reservoir: 40mM MgAc/50mM sodium cacodylate pH 6.0/30% (v/v) MPD; 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
5MgAc12
6sodium cacodylate12
7MPD12
8H2O12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 1.00605 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 7, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00605 Å / Relative weight: 1
ReflectionResolution: 2.64→50 Å / Num. obs: 23676 / % possible obs: 97.9 % / Redundancy: 7.6 % / Rsym value: 0.047 / Net I/σ(I): 36.2
Reflection shellResolution: 2.64→2.73 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 2.5 / Rsym value: 0.417 / % possible all: 83.1

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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: 2.64→42.57 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.91 / WRfactor Rfree: 0.29 / WRfactor Rwork: 0.237 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.78 / SU B: 13.804 / SU ML: 0.288 / SU R Cruickshank DPI: 0.684 / SU Rfree: 0.363 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.684 / ESU R Free: 0.363 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; MOST OF THE TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS, FALL INTO GENERALLY ALLOWED REGIONS, ONLY A MINORITY BELONGS TO THE DISALLOWED REGIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.29684 1213 5.1 %RANDOM
Rwork0.24046 ---
obs0.24319 22367 97.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 165.4 Å2 / Biso mean: 67.685 Å2 / Biso min: 38.78 Å2
Baniso -1Baniso -2Baniso -3
1-2.78 Å20 Å20 Å2
2---4.29 Å20 Å2
3---1.51 Å2
Refinement stepCycle: LAST / Resolution: 2.64→42.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4248 278 17 16 4559
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0224686
X-RAY DIFFRACTIONr_angle_refined_deg1.3352.0216375
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8325507
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.08822.72239
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.24115757
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2091546
X-RAY DIFFRACTIONr_chiral_restr0.090.2639
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023560
X-RAY DIFFRACTIONr_nbd_refined0.2110.22104
X-RAY DIFFRACTIONr_nbtor_refined0.3140.23105
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1770.2195
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2980.231
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2270.23
X-RAY DIFFRACTIONr_mcbond_it0.7081.52581
X-RAY DIFFRACTIONr_mcangle_it1.24624077
X-RAY DIFFRACTIONr_scbond_it1.17632483
X-RAY DIFFRACTIONr_scangle_it1.9524.52298
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDNumberTypeRms dev position (Å)Weight position
1181tight positional0.040.05
2157tight positional0.040.05
3544tight positional0.060.05
4153tight positional0.030.05
538tight positional0.030.05
6139tight positional00.05
7671tight positional0.050.05
886tight positional0.040.05
1181tight thermal1.820.5
2157tight thermal2.110.5
3544tight thermal1.830.5
4153tight thermal1.750.5
538tight thermal0.80.5
6139tight thermal00.5
7671tight thermal3.320.5
886tight thermal1.350.5
LS refinement shellResolution: 2.638→2.706 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 60 -
Rwork0.35 1325 -
all-1385 -
obs--78.47 %

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