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- PDB-1fw6: CRYSTAL STRUCTURE OF A TAQ MUTS-DNA-ADP TERNARY COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1fw6
TitleCRYSTAL STRUCTURE OF A TAQ MUTS-DNA-ADP TERNARY COMPLEX
Components
  • 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'
  • 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 / protein-DNA complex / multi-domain structure / kinked DNA / ABC ATPase / 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 / 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
ADENOSINE-5'-DIPHOSPHATE / DNA / DNA (> 10) / DNA mismatch repair protein MutS
Similarity search - Component
Biological speciesThermus aquaticus (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.7 Å
AuthorsJunop, M.S. / Obmolova, G. / Rausch, K. / Hsieh, P. / Yang, W.
CitationJournal: Mol.Cell / Year: 2001
Title: Composite active site of an ABC ATPase: MutS uses ATP to verify mismatch recognition and authorize DNA repair.
Authors: Junop, M.S. / Obmolova, G. / Rausch, K. / Hsieh, P. / Yang, W.
History
DepositionSep 21, 2000Deposition site: NDB / Processing site: NDB
Revision 1.0Feb 19, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: 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: 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)188,60012
Polymers187,3134
Non-polymers1,2878
Water4,107228
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)103.717, 113.496, 160.501
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe crystallographic dimer is the functional unit of MutS. A dimer of MutS binds a single mismatch in a heteroduplex DNA.

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Components

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DNA chain , 2 types, 2 molecules CD

#1: DNA chain 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 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


Mass: 86729.492 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-768
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 , 4 types, 236 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 228 / 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: 2.51 Å3/Da / Density % sol: 51.04 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 100 mM cacodylate, 200 mM ammonium sulfate, 1 mM DTT, 5 mM MgCl2, 20% PEG4000, 1 mM ATP, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 22K
Components of the solutions
IDNameCrystal-IDSol-ID
1cacodylate11
2(NH4)2SO411
3DTT11
4MgCl211
5PEG 400011
6ATP11
Crystal grow
*PLUS
Temperature: 20 ℃ / Details: Obmolova, G., (2000) Nature, 407, 703.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.5-15 mg/mlprotein1drop
2100 mMcacodylate1reservoir
3200 mMammonium sulfate1reservoir
41 mMdithiothreitol1reservoir
518 %PEG40001reservoir
61

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Dec 24, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→23.2 Å / Num. all: 52652 / Num. obs: 49041 / % possible obs: 93.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -1 / Redundancy: 2.4 % / Biso Wilson estimate: 38.3 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 10.3
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.324 / Num. unique all: 2605 / % possible all: 85.2
Reflection shell
*PLUS
% possible obs: 85.2 %

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementResolution: 2.7→23.17 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 186038.15 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -1 / Stereochemistry target values: Engh & Huber / Details: Used weighted full matrix least squares procedure
RfactorNum. reflection% reflectionSelection details
Rfree0.28 2397 5 %RANDOM
Rwork0.218 ---
all0.218 52652 --
obs0.218 47822 90.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 24.9 Å2 / ksol: 0.297 e/Å3
Displacement parametersBiso mean: 45.6 Å2
Baniso -1Baniso -2Baniso -3
1--14.67 Å20 Å20 Å2
2--6.62 Å20 Å2
3---8.05 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.46 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.56 Å0.46 Å
Refinement stepCycle: LAST / Resolution: 2.7→23.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11942 919 76 228 13165
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d22.3
X-RAY DIFFRACTIONc_improper_angle_d0.98
X-RAY DIFFRACTIONc_mcbond_it1.21.5
X-RAY DIFFRACTIONc_mcangle_it2.122
X-RAY DIFFRACTIONc_scbond_it1.622
X-RAY DIFFRACTIONc_scangle_it2.582.5
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.362 343 4.8 %
Rwork0.322 6764 -
obs--82.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3ION.PARAM
X-RAY DIFFRACTION4WATER_REP.PARA&_1_TOPOLOGY_INFILE_4
X-RAY DIFFRACTION5ADP.PARAMADP.TOP
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / Rfactor Rfree: 0.28
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 45.6 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.98
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.362 / % reflection Rfree: 4.8 % / Rfactor Rwork: 0.322

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