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- PDB-1cw0: CRYSTAL STRUCTURE ANALYSIS OF VERY SHORT PATCH REPAIR (VSR) ENDON... -

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Basic information

Entry
Database: PDB / ID: 1cw0
TitleCRYSTAL STRUCTURE ANALYSIS OF VERY SHORT PATCH REPAIR (VSR) ENDONUCLEASE IN COMPLEX WITH A DUPLEX DNA
Components
  • DNA (5'-D(*AP*CP*GP*TP*AP*CP*CP*TP*GP*GP*CP*T)-3')
  • DNA (5'-D(*AP*GP*C)-3')
  • DNA (5'-D(P*TP*AP*GP*GP*TP*AP*CP*GP*T)-3')
  • PROTEIN (DNA MISMATCH ENDONUCLEASE)
KeywordsHYDROLASE/DNA / PROTEIN-DNA COMPLEX / MISMATCH / INTERCALATION / ZINC / HYDROLASE-DNA complex
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 / Resolution: 2.3 Å
AuthorsTsutakawa, S.E. / Jingami, H. / Morikawa, K.
CitationJournal: Cell(Cambridge,Mass.) / Year: 1999
Title: Recognition of a TG mismatch: the crystal structure of very short patch repair endonuclease in complex with a DNA duplex.
Authors: Tsutakawa, S.E. / Jingami, H. / Morikawa, K.
History
DepositionAug 25, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 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_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_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_conn.ptnr2_label_seq_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
M: DNA (5'-D(*AP*CP*GP*TP*AP*CP*CP*TP*GP*GP*CP*T)-3')
N: DNA (5'-D(*AP*GP*C)-3')
O: DNA (5'-D(P*TP*AP*GP*GP*TP*AP*CP*GP*T)-3')
A: PROTEIN (DNA MISMATCH ENDONUCLEASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3247
Polymers25,2104
Non-polymers1143
Water3,711206
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.000, 63.000, 152.500
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Cell settinghexagonal
Space group name H-MP65

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Components

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DNA chain , 3 types, 3 molecules MNO

#1: DNA chain DNA (5'-D(*AP*CP*GP*TP*AP*CP*CP*TP*GP*GP*CP*T)-3')


Mass: 3638.379 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*AP*GP*C)-3')


Mass: 886.637 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain DNA (5'-D(P*TP*AP*GP*GP*TP*AP*CP*GP*T)-3')


Mass: 2770.834 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Protein , 1 types, 1 molecules A

#4: Protein PROTEIN (DNA MISMATCH ENDONUCLEASE) / VSR ENDONUCLEASE / PATCH REPAIR PROTEIN


Mass: 17914.473 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
References: UniProt: P09184, Hydrolases; Acting on ester bonds

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Non-polymers , 3 types, 209 molecules

#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 206 / 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: 3.47 Å3/Da / Density % sol: 64.51 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 5.6 / Details: pH 5.60, VAPOR DIFFUSION, HANGING DROP
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
11.5 mMDNA11
20.5 mMprotein11
320 mM11MgCl2
42.5 %PEG800011
525 mMMES11
6100 mM11KCl
715 mM11MgCl2
86.5 mMTris-HCl11
931.0 mM11NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL24XU / Wavelength: 0.834
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Jun 10, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.834 Å / Relative weight: 1
ReflectionResolution: 2.3→24.254 Å / Num. obs: 15166 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 4.6 % / Biso Wilson estimate: 28.5 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 14.4
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.316 / % possible all: 100
Reflection
*PLUS
Lowest resolution: 22 Å / Num. obs: 15168 / % possible obs: 99.4 % / Rmerge(I) obs: 0.048
Reflection shell
*PLUS
% possible obs: 100 % / Rmerge(I) obs: 0.261

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Processing

Software
NameClassification
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementStarting model: TRUNCATED VSR MODEL, 1VSR

1vsr


Resolution: 2.3→22 Å / Rfactor Rfree error: 0.008 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.23 753 5 %RANDOM
Rwork0.204 ---
obs0.204 14332 94.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.36 Å2 / ksol: 0.322 e/Å3
Displacement parametersBiso mean: 31.8 Å2
Baniso -1Baniso -2Baniso -3
1-2.87 Å25.97 Å20 Å2
2--2.87 Å20 Å2
3----5.74 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 2.3→22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1260 488 3 206 1957
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
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_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.86
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.181.5
X-RAY DIFFRACTIONc_mcangle_it1.852
X-RAY DIFFRACTIONc_scbond_it1.822
X-RAY DIFFRACTIONc_scangle_it2.642.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.28 116 4.6 %
Rwork0.243 2384 -
obs--98.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN-ALLHDG.PARAMPROTEIN-ALLHDG.TOP
X-RAY DIFFRACTION2DNA-RNA-ALLATOM.PARAMDNA-RNA-ALLATOM.TOP
Software
*PLUS
Name: 'CNS' / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.86

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