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- PDB-1ewq: CRYSTAL STRUCTURE TAQ MUTS COMPLEXED WITH A HETERODUPLEX DNA AT 2... -

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Basic information

Entry
Database: PDB / ID: 1ewq
TitleCRYSTAL STRUCTURE TAQ MUTS COMPLEXED WITH A HETERODUPLEX DNA AT 2.2 A RESOLUTION
Components
  • DNA (5'-D(*GP*CP*GP*AP*CP*GP*CP*TP*AP*GP*CP*GP*TP*GP*CP*GP*GP*CP*TP*CP*GP*TP*C)-3')
  • DNA (5'-D(*GP*GP*AP*CP*GP*AP*GP*CP*CP*GP*CP*CP*GP*CP*TP*AP*GP*CP*GP*TP*CP*G)-3')
  • DNA MISMATCH REPAIR PROTEIN MUTS
Keywordsreplication/DNA / Multiple domains of protein / mostly mixed alpha-beta structures / one domain is entirely helical / double stranded helix / replication-DNA COMPLEX
Function / homology
Function and homology information


mismatched DNA binding / ATP-dependent DNA damage sensor activity / mismatch repair / damaged DNA binding / ATP binding
Similarity search - Function
MutS, connector domain / DNA repair protein MutS, domain I / MutS, DNA mismatch repair protein; Chain A, domain 3 / MutS, DNA mismatch repair protein; Chain A, domain 3 - #10 / DNA mismatch repair protein MutS / DNA mismatch repair protein MutS/MSH / DNA mismatch repair protein MutS-like, N-terminal / DNA mismatch repair protein MutS, connector domain / DNA mismatch repair protein MutS, clamp / DNA mismatch repair protein MutS, N-terminal ...MutS, connector domain / DNA repair protein MutS, domain I / MutS, DNA mismatch repair protein; Chain A, domain 3 / MutS, DNA mismatch repair protein; Chain A, domain 3 - #10 / DNA mismatch repair protein MutS / DNA mismatch repair protein MutS/MSH / DNA mismatch repair protein MutS-like, N-terminal / DNA mismatch repair protein MutS, connector domain / DNA mismatch repair protein MutS, clamp / DNA mismatch repair protein MutS, N-terminal / MutS, connector domain superfamily / MutS domain I / MutS domain II / MutS family domain IV / MutS domain III / DNA mismatch repair MutS family / DNA mismatch repair protein MutS, C-terminal / DNA mismatch repair protein MutS, core / DNA mismatch repair protein MutS, core domain superfamily / MutS domain V / DNA mismatch repair proteins mutS family signature. / DNA-binding domain of DNA mismatch repair MUTS family / ATPase domain of DNA mismatch repair MUTS family / MutS, DNA mismatch repair protein, domain I / Nucleotidyltransferase; domain 5 / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA mismatch repair protein MutS
Similarity search - Component
Biological speciesThermus aquaticus (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsObmolova, G. / Ban, C. / Hsieh, P. / Yang, W.
CitationJournal: Nature / Year: 2000
Title: Crystal structures of mismatch repair protein MutS and its complex with a substrate DNA.
Authors: Obmolova, G. / Ban, C. / Hsieh, P. / Yang, W.
History
DepositionApr 26, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Nov 3, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _struct_conn.pdbx_leaving_atom_flag / _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
C: DNA (5'-D(*GP*CP*GP*AP*CP*GP*CP*TP*AP*GP*CP*GP*TP*GP*CP*GP*GP*CP*TP*CP*GP*TP*C)-3')
D: DNA (5'-D(*GP*GP*AP*CP*GP*AP*GP*CP*CP*GP*CP*CP*GP*CP*TP*AP*GP*CP*GP*TP*CP*G)-3')
A: DNA MISMATCH REPAIR PROTEIN MUTS
B: DNA MISMATCH REPAIR PROTEIN MUTS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)187,44515
Polymers186,6264
Non-polymers81911
Water14,664814
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)103.167, 114.216, 160.792
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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Components

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DNA chain , 2 types, 2 molecules CD

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


Mass: 7074.534 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*GP*GP*AP*CP*GP*AP*GP*CP*CP*GP*CP*CP*GP*CP*TP*AP*GP*CP*GP*TP*CP*G)-3')


Mass: 6779.355 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Protein , 1 types, 2 molecules AB

#3: Protein DNA MISMATCH REPAIR PROTEIN MUTS / / TAQ MUTS SUBUNIT A


Mass: 86386.125 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus aquaticus (bacteria) / Plasmid: PET3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q56215

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Non-polymers , 3 types, 825 molecules

#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 814 / 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: 2.53 Å3/Da / Density % sol: 51.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: PEG 4000, cacodylate, MgCl2, (NH4)2SO4, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1cacodylateCacodylic acid11
2MgCl211
3(NH4)2SO411
4PEG 400011
5PEG 400012
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.5-15 mg/mlprotein1drop
2100 mMcacodylate1reservoir
3200 mMammonium sulfate1reservoir
41 mMdithiothreitol1reservoir
518 %PEG40001reservoir

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 8, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. all: 93885 / Num. obs: 91291 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 26.5 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 16
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.309 / Num. unique all: 4304 / % possible all: 90.9
Reflection shell
*PLUS
% possible obs: 90.9 %

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Processing

Software
NameVersionClassification
SOLVEphasing
CNS0.9refinement
SCALEPACKdata scaling
RefinementResolution: 2.2→26.6 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 447159.04 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.259 4665 5 %RANDOM
Rwork0.227 ---
all0.227 93885 --
obs0.227 92703 95.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 41.54 Å2 / ksol: 0.337 e/Å3
Displacement parametersBiso mean: 38.7 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å20 Å20 Å2
2--3.98 Å20 Å2
3----3.79 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.28 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 2.2→26.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11947 919 48 814 13728
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22
X-RAY DIFFRACTIONc_improper_angle_d0.89
X-RAY DIFFRACTIONc_mcbond_it0.541.5
X-RAY DIFFRACTIONc_mcangle_it0.992
X-RAY DIFFRACTIONc_scbond_it0.62
X-RAY DIFFRACTIONc_scangle_it0.982.5
LS refinement shellResolution: 2→2.13 Å / Total num. of bins used: 6 /
RfactorNum. reflection
Rwork0.259 0
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PAPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PADNA-RNA.TOP
X-RAY DIFFRACTION3ION.PARAM
X-RAY DIFFRACTION4WATER_REP.PARA&_1_TOPOLOGY_INFILE_4
X-RAY DIFFRACTION5EDO.PARAMEDO.TOP
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.89

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