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- PDB-1ewr: CRYSTAL STRUCTURE OF TAQ MUTS -

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Basic information

Entry
Database: PDB / ID: 1ewr
TitleCRYSTAL STRUCTURE OF TAQ MUTS
ComponentsDNA MISMATCH REPAIR PROTEIN MUTS
KeywordsHYDROLASE / DNA repair / DNA-binding / ATP-binding
Function / homology
Function and homology information


mismatched DNA binding / ATP-dependent DNA damage sensor activity / mismatch repair / damaged DNA binding / ATP binding / cytosol
Similarity search - Function
MutS, connector domain / 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, connector domain / 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 / Nucleotidyltransferase; domain 5 / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA mismatch repair protein MutS
Similarity search - Component
Biological speciesThermus aquaticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.19 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 1.3Jun 27, 2018Group: Data collection / Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA MISMATCH REPAIR PROTEIN MUTS
B: DNA MISMATCH REPAIR PROTEIN MUTS


Theoretical massNumber of molelcules
Total (without water)146,0972
Polymers146,0972
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3940 Å2
ΔGint-43 kcal/mol
Surface area41990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.734, 96.734, 427.126
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
DetailsThe biological assembly is a dimer composed of chain A and chain B

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Components

#1: Protein DNA MISMATCH REPAIR PROTEIN MUTS


Mass: 73048.641 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus aquaticus (bacteria) / Description: WHOLE CELL / Production host: Escherichia coli (E. coli) / References: UniProt: Q56215

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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: 3.95 Å3/Da / Density % sol: 68.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: PEG 400, ammonium sulfate, copper chloride, HEPES, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 27 ℃ / pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
140 mg/mlprotein1drop
220 mMTris-HCl1drop
3200 mM1dropKCl
41 mMdithiothreitol1drop
50.1 mMEDTA1d
65 mM1dropMgSO4
75 %glycerol1drop
890 mMHEPES1reservoir
97.2 %PEG4001reservoir
101.8 Mammonium sulfate1reservoir
111.5 mM1reservoirCuCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.987
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 1, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 3.2→30 Å / Num. all: 34848 / Num. obs: 30381 / % possible obs: 88.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 82.5 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 16.1
Reflection shellResolution: 3.2→3.25 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.443 / Num. unique all: 1618 / % possible all: 85.3
Reflection shell
*PLUS
% possible obs: 85.3 %

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementResolution: 3.19→19.94 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 312339.53 / 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
Rfree0.361 3385 4.9 %RANDOM
Rwork0.331 ---
all0.331 34848 --
obs0.331 30381 93 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 28.55 Å2 / ksol: 0.263 e/Å3
Displacement parametersBiso mean: 101.2 Å2
Baniso -1Baniso -2Baniso -3
1--21.71 Å2-0.04 Å20 Å2
2---21.71 Å20 Å2
3---43.42 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.56 Å0.49 Å
Luzzati d res low-5 Å
Luzzati sigma a0.87 Å0.81 Å
Refinement stepCycle: LAST / Resolution: 3.19→19.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7594 0 0 0 7594
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d22.4
X-RAY DIFFRACTIONc_improper_angle_d1
X-RAY DIFFRACTIONc_mcbond_it8.661.5
X-RAY DIFFRACTIONc_mcangle_it13.392
X-RAY DIFFRACTIONc_scbond_it11.482
X-RAY DIFFRACTIONc_scangle_it16.072.5
LS refinement shellResolution: 2→2.13 Å / Total num. of bins used: 6 /
RfactorNum. reflection
Rwork0.361 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 DIFFRACTION4&_1_TOPOLOGY_INFILE_4
X-RAY DIFFRACTION5EDO.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_deg22.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1

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