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- PDB-3g2d: Complex of Mth0212 and a 4 bp dsDNA with 3'-overhang -

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Basic information

Entry
Database: PDB / ID: 3g2d
TitleComplex of Mth0212 and a 4 bp dsDNA with 3'-overhang
Components
  • 5'-D(*CP*CP*TP*GP*UP*GP*CP*GP*AP*T)-3'
  • 5'-D(*CP*GP*CP*G*CP*AP*GP*GP*C)-3'
  • Exodeoxyribonuclease
KeywordsHYDROLASE/DNA / protein-DNA complex / dsDNA with 3'-overhang / HYDROLASE-DNA COMPLEX
Function / homology
Function and homology information


exodeoxyribonuclease III / double-stranded DNA 3'-5' DNA exonuclease activity / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / endonuclease activity / DNA repair / 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 / struct_ncs_dom_lim / struct_ref_seq / 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_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.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 285CRYST1 THE DEPOSITOR CONFIRM THE REPORTED SPACE GROUP P 1 21 1 DESPITE OF THE BETA ANGLE OF 90.0 ...CRYST1 THE DEPOSITOR CONFIRM THE REPORTED SPACE GROUP P 1 21 1 DESPITE OF THE BETA ANGLE OF 90.0 DEGREE. THE STRUCTURE COULD NOT BE REFINED IN A PRIMITIVE ORTHORHOMBIC SPACE GROUP - MOST LIKELY DUE TO SOME DISORDER IN THE CRYSTAL OR TWINNING. HOWEVER, THERE WAS NO INDICATION OF TWINNING. THE PRESENCE OF PEG MOLECULES IN ONLY ONE OF THE TWO PROTEIN MOLECULES IN THE ASYMMETRIC UNIT (ASU) AT EQUIVALENT POSITIONS (IN SPACE GROUP P21) AND DIFFERENCES IN THE DOUBLE-STRANDED DNA HELICES (DIFFERENT LENGTH OF ONE STRAND) BOUND BY THE TWO MOLECULES IN THE ASU E.G. ARGUED AGAINST MODEL BUILDING IN AN ORTHORHOMBIC SPACE GROUP. HOWEVER, THE USE OF A TWIN LAW MIGHT HAVE BEEN AN ADVANTAGE, BUT WAS NOT TAKEN INTO ACCOUNT DUE TO THE RESOLUTION OF 2.3A PREVENTING REFINEMENT WITH SHELXL AND DNA RESTRAINTS IN CNS LESS SUITABLE THAN THE RESTRAINTS USED BY REFMAC5 FOR EXAMPLE. THE STRUCTURE COULD BE REFINED TO REASONABLE R VALUES EVEN WITHOUT THE APPLICATION OF A TWIN LAW. THUS, THE REFINEMENT WAS CONTINUED IN THE SPACE GROUP P21.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)76,09320
Polymers74,3876
Non-polymers1,70614
Water5,639313
1
A: Exodeoxyribonuclease
G: 5'-D(*CP*GP*CP*G*CP*AP*GP*GP*C)-3'
K: 5'-D(*CP*CP*TP*GP*UP*GP*CP*GP*AP*T)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,61415
Polymers37,1933
Non-polymers1,42012
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2020 Å2
ΔGint-9 kcal/mol
Surface area12750 Å2
MethodPISA
2
B: Exodeoxyribonuclease
H: 5'-D(*CP*GP*CP*G*CP*AP*GP*GP*C)-3'
I: 5'-D(*CP*CP*TP*GP*UP*GP*CP*GP*AP*T)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4805
Polymers37,1933
Non-polymers2862
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2010 Å2
ΔGint-8 kcal/mol
Surface area13060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.603, 81.301, 97.091
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / Refine code: 1

Dom-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1LEULEUAA2 - 2572 - 257
2GLUGLUBB2 - 2562 - 256

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Exodeoxyribonuclease / / Mth0212


Mass: 31429.666 Da / Num. of mol.: 2 / 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

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DNA chain , 2 types, 4 molecules GHKI

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


Mass: 2741.800 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: DNA chain 5'-D(*CP*CP*TP*GP*UP*GP*CP*GP*AP*T)-3'


Mass: 3021.964 Da / Num. of mol.: 2 / Source method: obtained synthetically

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Non-polymers , 4 types, 327 molecules

#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#5: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 313 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsTHE 3'-OVERHANG OF THE DNA COMPRISES 4 AND 5 NUCLEOTIDES, RESPECTIVELY, ADJACENT TO THE TWO DOUBLE- ...THE 3'-OVERHANG OF THE DNA COMPRISES 4 AND 5 NUCLEOTIDES, RESPECTIVELY, ADJACENT TO THE TWO DOUBLE-HELICES OF THE ASYMMETRIC UNIT. ALL DNA OLIGONUCLEOTIDES USED FOR CRYSTALLIZATION HAVE BEEN PARTIALLY DEGRADED OR CONTAIN ONE OR MORE DISORDERED NUCLEOTIDES.

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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: 2.37 Å3/Da / Density % sol: 48.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.8
Details: reservoir: 5% (w/v) PEG 4000, 50mM KCl, 50mM MES pH 5.8, 10mM MgCl2 ; complex solution: 240mM NaCl, 8mM HEPES-KOH pH 7.6, 4mM DTT, 2mM MgCl2, 1mM KH2PO4/K2HPO4 pH 7.0, VAPOR DIFFUSION, ...Details: reservoir: 5% (w/v) PEG 4000, 50mM KCl, 50mM MES pH 5.8, 10mM MgCl2 ; complex solution: 240mM NaCl, 8mM HEPES-KOH pH 7.6, 4mM DTT, 2mM MgCl2, 1mM KH2PO4/K2HPO4 pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1NaClSodium chloride11
2HEPES-KOH11
3DTT11
4MgCl211
5KH2PO4/K2HPO411
6H2O11
7PEG 400012
8KCl12
9MES12
10MgCl212
11H2O12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.815 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 27, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.815 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 29120 / % possible obs: 93.8 % / Redundancy: 2.9 % / Rsym value: 0.055 / Net I/σ(I): 18
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 4.2 / Rsym value: 0.191 / % possible all: 76.3

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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→48.55 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.862 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.787 / SU B: 7.971 / SU ML: 0.198 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.445 / ESU R Free: 0.289 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27938 1470 5.1 %RANDOM
Rwork0.21421 ---
obs0.21747 27632 93.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 107.75 Å2 / Biso mean: 28.354 Å2 / Biso min: 9.4 Å2
Baniso -1Baniso -2Baniso -3
1--1.79 Å20 Å20.12 Å2
2---2.51 Å20 Å2
3---4.3 Å2
Refinement stepCycle: LAST / Resolution: 2.3→48.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4262 501 109 313 5185
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0225039
X-RAY DIFFRACTIONr_angle_refined_deg1.4182.0926867
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5095511
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.34822.78241
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.77415759
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4291546
X-RAY DIFFRACTIONr_chiral_restr0.0950.2685
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213703
X-RAY DIFFRACTIONr_mcbond_it0.5651.52542
X-RAY DIFFRACTIONr_mcangle_it1.06224098
X-RAY DIFFRACTIONr_scbond_it1.4532497
X-RAY DIFFRACTIONr_scangle_it2.2914.52768
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 2122 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
tight positional0.020.05
tight thermal0.080.5
LS refinement shellResolution: 2.296→2.356 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 92 -
Rwork0.256 1601 -
all-1693 -
obs--73.26 %

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