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- PDB-1odg: Very-short-patch DNA repair endonuclease bound to its reaction pr... -

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Basic information

Entry
Database: PDB / ID: 1odg
TitleVery-short-patch DNA repair endonuclease bound to its reaction product site
Components
  • 5'-D(*TP*AP*GP*GP*CP*5CM*TP*GP*GP*AP*TP*CP)-3'
  • DNA MISMATCH ENDONUCLEASE
KeywordsHYDROLASE / DNA REPAIR / ENDONUCLEASE / VERY SHORT PATCH REPAIR / DNA REPAI HYDROLASE / NUCLEASE / ZINC / METAL-BINDING
Function / homology
Function and homology information


T/G mismatch-specific endonuclease activity / mismatch repair / Hydrolases; Acting on ester bonds / DNA binding / metal ion binding
Similarity search - Function
DNA mismatch endonuclease VSR / DNA mismatch endonuclease Vsr / Endonuclease; Chain A / VSR Endonuclease / Restriction endonuclease type II-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA mismatch endonuclease Vsr
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsBunting, K.A. / Roe, S.M. / Headley, A. / Brown, T. / Savva, R. / Pearl, L.H.
CitationJournal: Nucleic Acids Res. / Year: 2003
Title: Crystal Structure of the Escherichia Coli Dcm Very-Short-Patch DNA Repair Endonuclease Bound to its Reaction Product-Site in a DNA Superhelix
Authors: Bunting, K.A. / Roe, S.M. / Headley, A. / Brown, T. / Savva, R. / Pearl, L.H.
History
DepositionFeb 19, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 13, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_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.conn_type_id / _struct_conn.id / _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_conn_type.id / _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: DNA MISMATCH ENDONUCLEASE
F: 5'-D(*TP*AP*GP*GP*CP*5CM*TP*GP*GP*AP*TP*CP)-3'
W: 5'-D(*TP*AP*GP*GP*CP*5CM*TP*GP*GP*AP*TP*CP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0194
Polymers22,9543
Non-polymers651
Water1,45981
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)102.805, 102.805, 64.290
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
DetailsTHE TRIMERIC ASSEMBLY DESCRIBED HERE IS FORMED BYTHE COMPLEX OF PROTEIN CHAIN A WITH DNA CHAINS F,W

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Components

#1: Protein DNA MISMATCH ENDONUCLEASE / VERY SHORT PATCH REPAIR PROTEIN / VSR MISMATCH ENDONUCLEASE / V.ECOKDCM / VSR / B1960


Mass: 15568.826 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Plasmid: PET28 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834 (DE3) / References: UniProt: P09184
#2: DNA chain 5'-D(*TP*AP*GP*GP*CP*5CM*TP*GP*GP*AP*TP*CP)-3'


Mass: 3692.430 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli)
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / Source method: isolated from a natural source / Formula: H2O
Compound detailsFUNCTIONS IN THE DEAMINATION OF 5-METHYLCYTOSINE IN DNA CAUSING MISMATCHES IN T/G WHICH CAN LEAD TO ...FUNCTIONS IN THE DEAMINATION OF 5-METHYLCYTOSINE IN DNA CAUSING MISMATCHES IN T/G WHICH CAN LEAD TO C-TO-T TRANSITION MUTATIONS IF UNREPAIRED.

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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: 4.2 Å3/Da / Density % sol: 70.7 %
Crystal growpH: 6.5
Details: 25 MM HEPES PH7.0, 75 MM NACL, 15% PEG 8000, 50 MM SODIUM CACODYLATE PH 6.5, 75 MM AMMONIUM SULPHATE AND 10% GLYCEROL PROTEIN 2.5 MG/ML
Crystal grow
*PLUS
Temperature: 14 ℃ / Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
125 mMHEPES11pH7.0
275 mM11NaCl
315 %PEG800011
450 mMsodium cacodylate11pH6.5
575 mMammonium sulfate11
610 %glycerol11
72.5 mg/mlprotein11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 15, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.75→50 Å / Num. obs: 10084 / % possible obs: 99 % / Redundancy: 4.9 % / Biso Wilson estimate: 105 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 6.9
Reflection shellResolution: 2.75→2.9 Å / Redundancy: 5 % / Rmerge(I) obs: 0.384 / Mean I/σ(I) obs: 2 / % possible all: 100
Reflection
*PLUS
Rmerge(I) obs: 0.07
Reflection shell
*PLUS
% possible obs: 100 % / Num. unique obs: 1464

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Processing

Software
NameVersionClassification
CNS1refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CW0

1cw0


Resolution: 2.8→24.7 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.3561 923 10 %RANDOM
Rwork0.2873 ---
obs0.2873 9535 98.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 74.25 Å2 / ksol: 0.318 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--15.19 Å2-6.172 Å20 Å2
2---15.19 Å20 Å2
3---30.38 Å2
Refinement stepCycle: LAST / Resolution: 2.8→24.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1092 498 1 81 1672
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008265
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.30641
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.3721.5
X-RAY DIFFRACTIONc_mcangle_it2.3812
X-RAY DIFFRACTIONc_scbond_it2.3252
X-RAY DIFFRACTIONc_scangle_it3.9632.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2LHP_DNA-RNA.PARAMLHP_DNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
Refinement
*PLUS
Rfactor Rfree: 0.356 / Rfactor Rwork: 0.287
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.306

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