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- PDB-1e3m: The crystal structure of E. coli MutS binding to DNA with a G:T m... -

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Entry
Database: PDB / ID: 1e3m
TitleThe crystal structure of E. coli MutS binding to DNA with a G:T mismatch
Components
  • 5'-D(*AP*GP*CP*TP*GP*CP*CP*AP*GP*GP*CP*AP*CP*CP*AP* GP*TP*GP*TP*CP*AP*GP*CP*GP*TP*CP*CP*TP*AP*T)-3'
  • 5'-D(*AP*TP*AP*GP*GP*AP*CP*GP*CP*TP*GP*AP*CP*AP*CP* TP*GP*GP*TP*GP*CP*TP*TP*GP*GP*CP*AP*GP*CP*T)-3'
  • DNA MISMATCH REPAIR PROTEIN MUTS
KeywordsDNA BINDING / MISMATCH RECOGNITION
Function / homologyDNA 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 / DNA mismatch repair protein MutS, C-terminal / DNA mismatch repair protein MutS, N-terminal / DNA mismatch repair protein MutS/MSH / P-loop containing nucleoside triphosphate hydrolase / DNA mismatch repair protein MutS, core domain superfamily / MutS, connector domain superfamily ...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 / DNA mismatch repair protein MutS, C-terminal / DNA mismatch repair protein MutS, N-terminal / DNA mismatch repair protein MutS/MSH / P-loop containing nucleoside triphosphate hydrolase / DNA mismatch repair protein MutS, core domain superfamily / MutS, connector domain superfamily / MutS domain V / MutS domain I / MutS domain II / MutS family domain IV / MutS domain III / DNA mismatch repair proteins mutS family signature. / DNA mismatch repair protein MutS, core / adenine/cytosine mispair binding / regulation of DNA recombination / mismatch repair complex / mismatched DNA binding / DNA binding, bending / DNA-dependent ATPase activity / mismatch repair / ADP binding / ATPase activity / damaged DNA binding / cellular response to DNA damage stimulus / ATP binding / identical protein binding / cytosol / DNA mismatch repair protein MutS
Function and homology information
Specimen sourceESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / 2.2 Å resolution
AuthorsLamers, M.H. / Perrakis, A. / Enzlin, J.H. / Winterwerp, H.H.K. / De Wind, N. / Sixma, T.K.
CitationJournal: Nature / Year: 2000
Title: The Crystal Structure of DNA Mismatch Repair Protein Muts Binding to a G X T Mismatch
Authors: Lamers, M.H. / Perrakis, A. / Enzlin, J.H. / Winterwerp, H.H.K. / De Wind, N. / Sixma, T.K.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jun 19, 2000 / Release: Nov 1, 2000
RevisionDateData content typeGroupCategoryItemProviderType
1.0Nov 1, 2000Structure modelrepositoryInitial release
1.1Feb 5, 2014Structure modelDatabase references / Derived calculations / Non-polymer description / Other / Refinement description / Source and taxonomy / Structure summary / Version format compliance
1.2Jul 5, 2017Structure modelRefinement descriptionsoftware_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA MISMATCH REPAIR PROTEIN MUTS
B: DNA MISMATCH REPAIR PROTEIN MUTS
E: 5'-D(*AP*GP*CP*TP*GP*CP*CP*AP*GP*GP*CP*AP*CP*CP*AP* GP*TP*GP*TP*CP*AP*GP*CP*GP*TP*CP*CP*TP*AP*T)-3'
F: 5'-D(*AP*TP*AP*GP*GP*AP*CP*GP*CP*TP*GP*AP*CP*AP*CP* TP*GP*GP*TP*GP*CP*TP*TP*GP*GP*CP*AP*GP*CP*T)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)200,4007
Polyers199,9254
Non-polymers4763
Water8,611478
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)11350
ΔGint (kcal/M)-95.7
Surface area (Å2)70310
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)89.960, 92.370, 261.330
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP 21 21 21

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Components

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Protein/peptide , 1 types, 2 molecules AB

#1: Protein/peptide DNA MISMATCH REPAIR PROTEIN MUTS /


Mass: 90729.859 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-800 / Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Cellular location: NUCLEUSCell nucleus / Gene: MUTSMutS-1 / Cellular location (production host): CYTOPLASM / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): PLYSS / References: UniProt: P23909

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DNA chain , 2 types, 2 molecules EF

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


Mass: 9184.905 Da / Num. of mol.: 1 / Details: G\:T MISMATCH DNA / Source: (synth.) ESCHERICHIA COLI (E. coli) / Details: DNA OLIGONUCLEOTIDES, ANNEALED
#3: DNA chain 5'-D(*AP*TP*AP*GP*GP*AP*CP*GP*CP*TP*GP*AP*CP*AP*CP* TP*GP*GP*TP*GP*CP*TP*TP*GP*GP*CP*AP*GP*CP*T)-3'


Mass: 9279.964 Da / Num. of mol.: 1 / Source: (synth.) ESCHERICHIA COLI (E. coli) / Details: DNA OLIGONUCLEOTIDES, ANNEALED

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Non-polymers , 3 types, 481 molecules

#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Formula: C10H15N5O10P2 / Adenosine diphosphate / Comment: ADP (energy-carrying molecule) *YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Formula: Mg / Magnesium
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 478 / Formula: H2O / Water

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Details

Compound detailsFUNCTION: THIS PROTEIN IS INVOLVED IN THE REPAIR OF MISMATCHES IN DNA. IT IS POSSIBLE THAT IT CARRY ...FUNCTION: THIS PROTEIN IS INVOLVED IN THE REPAIR OF MISMATCHES IN DNA. IT IS POSSIBLE THAT IT CARRY OUT THE MISMATCH RECOGNITION STEP. THIS PROTEIN HAS A WEAK ATPASE ACTIVITY. SIMILARITY: BELONGS TO THE DNA MISMATCH REPAIR MUTS FAMILY.

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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: 2.7 / Density percent sol: 55 % / Description: MAD DATA WERE COLLECTED IN ESRF BM14
Crystal growpH: 7
Details: 12-14 % PEG 6000, 150-300 MM NACL, 100 MM HEPES PH 7-8, 10 MM MGCL2, 100-150 MICROM ADP
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop / Details: used microseeding
components of the solutions
*PLUS
IDConcCommon nameCrystal IDSol IDChemical formula
114 mg/mlprotein1drop
225 mMHEPES1drop
3250 mM1dropNaCl
410-20 mMbeta-mercaptoethanol1drop
512-14 %PEG60001reservoir
6150-300 mM1reservoirNaCl
7100 mMHEPES1reservoir
810 mM1reservoirMgCl2
90.100-0.150 mMADP1reservoir

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Data collection

DiffractionMean temperature: 1
SourceSource: SYNCHROTRON / Type: ESRF BEAMLINE ID14-2 / Synchrotron site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: MARRESEARCH / Detector: CCD / Collection date: Feb 15, 2000
RadiationMonochromator: SI111 / Diffraction protocol: MAD / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 / Relative weight: 1
ReflectionD resolution high: 2.2 / D resolution low: 2 / Number obs: 109670 / Rmerge I obs: 0.065 / NetI over sigmaI: 15.9 / Redundancy: 3.7 % / Percent possible obs: 98.7
Reflection shellRmerge I obs: 0.469 / Highest resolution: 2.2 / Lowest resolution: 2.24 / MeanI over sigI obs: 2.2 / Redundancy: 3.1 % / Percent possible all: 95.1
Reflection shell
*PLUS
Percent possible obs: 95.1

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Processing

Software
NameVersionClassification
REFMAC5.0refinement
HKL-2000data reduction
HKL-2000data scaling
SnBphasing
MLPHAREphasing
SHARPphasing
RefineMethod to determine structure: MAD / Overall SU B: 7.181 / Overall SU ML: 0.183 / R Free selection details: RANDOM / Cross valid method: THROUGHOUT / Sigma F: 0 / Overall ESU R: 0.253 / Overall ESU R Free: 0.209 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Displacement parametersB iso mean: 46.62 / Aniso B11: -1.06 / Aniso B12: 0 / Aniso B13: 0 / Aniso B22: 3.76 / Aniso B23: 0 / Aniso B33: -2.7
Least-squares processR factor R free: 0.266 / R factor R work: 0.228 / R factor obs: 0.229 / Highest resolution: 2.2 / Lowest resolution: 2 / Number reflection R free: 2197 / Number reflection obs: 107405 / Percent reflection R free: 2 / Percent reflection obs: 98.7
Refine hist #LASTHighest resolution: 2.2 / Lowest resolution: 2
Number of atoms included #LASTProtein: 12171 / Nucleic acid: 714 / Ligand: 29 / Solvent: 478 / Total: 13392
Software
*PLUS
Name: REFMAC / Version: 5 / Classification: refinement
Displacement parameters
*PLUS
B iso mean: 46.622
Least-squares process
*PLUS
R factor R free: 0.26613 / R factor R work: 0.22814 / R factor obs: 0.22891
Refine LS restraints
*PLUS
Refine IDTypeDev idealWeight
X-RAY DIFFRACTIONp_bond_d0.012
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.173
X-RAY DIFFRACTIONp_mcbond_it1.500
X-RAY DIFFRACTIONp_scbond_it3.000
X-RAY DIFFRACTIONp_mcangle_it2.000
X-RAY DIFFRACTIONp_scangle_it4.500
Refine LS shell
*PLUS
R factor obs: 0.324 / R factor R free: 0.367

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