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- PDB-3k0s: Crystal structure of E.coli DNA mismatch repair protein MutS, D69... -

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Basic information

Entry
Database: PDB / ID: 3k0s
TitleCrystal structure of E.coli DNA mismatch repair protein MutS, D693N mutant, in complex with GT mismatched DNA
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*C*AP*CP*T*GP*GP*TP*GP*CP*TP*TP*GP*GP*CP*AP*GP*CP*T)-3'
  • DNA mismatch repair protein mutS
KeywordsDNA BINDING PROTEIN/DNA / Magnesium mutant / DNA repair protein / Protein-DNA complex / ATP-binding / DNA damage / DNA repair / DNA-binding / Nucleotide-binding / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


adenine/cytosine mispair binding / MutS complex / mismatch repair complex / regulation of DNA recombination / mismatched DNA binding / DNA binding, bending / ATP-dependent DNA damage sensor activity / mismatch repair / ADP binding / damaged DNA binding ...adenine/cytosine mispair binding / MutS complex / mismatch repair complex / regulation of DNA recombination / mismatched DNA binding / DNA binding, bending / ATP-dependent DNA damage sensor activity / mismatch repair / ADP binding / damaged DNA binding / DNA damage response / ATP hydrolysis activity / ATP binding / identical protein binding / cytosol
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 speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsReumer, G.A. / Winterwerp, H.H.K. / Sixma, T.K.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Magnesium coordination controls the molecular switch function of DNA mismatch repair protein MutS.
Authors: Lebbink, J.H. / Fish, A. / Reumer, A. / Natrajan, G. / Winterwerp, H.H. / Sixma, T.K.
History
DepositionSep 25, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Oct 13, 2021Group: Database references / Derived calculations / Category: database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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
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*C*AP*CP*T*GP*GP*TP*GP*CP*TP*TP*GP*GP*CP*AP*GP*CP*T)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)197,8365
Polymers197,4094
Non-polymers4271
Water13,854769
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11390 Å2
ΔGint-76 kcal/mol
Surface area68940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.604, 90.791, 261.191
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsBiological unit is the same as asymmetric unit. The word "tetrameric" in remark 350 is incorrect as it is only a chain count.

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Components

#1: Protein DNA mismatch repair protein mutS


Mass: 89472.172 Da / Num. of mol.: 2 / Fragment: UNP residues 2-800 / Mutation: D693N
Source method: isolated from a genetically manipulated source
Details: Original plasmid pMQ372 from M. Marinus / Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: b2733, fdv, JW2703, mutS / Plasmid: pET3D / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3)pLysS / References: UniProt: P23909
#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 / Source method: obtained synthetically / Details: Synthetic construct
#3: DNA chain 5'-D(*AP*TP*AP*GP*GP*AP*CP*GP*CP*TP*GP*AP*C*AP*CP*T*GP*GP*TP*GP*CP*TP*TP*GP*GP*CP*AP*GP*CP*T)-3'


Mass: 9279.964 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic construct
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 769 / 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: 2.69 Å3/Da / Density % sol: 54.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 11% PEG 6000, 750mM NaCl, 25mM Hepes, 10mM MgCl2, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 600011
2NaCl11
3Hepes11
4MgCl211
5PEG 600012
6NaCl12
7Hepes12
8MgCl212

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9775 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 25, 2008 / Details: toroidal mirror
RadiationMonochromator: Double crystal, Si(111) or Si(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9775 Å / Relative weight: 1
ReflectionResolution: 2.2→89.44 Å / Num. obs: 104793 / % possible obs: 96.4 % / Redundancy: 4.4 % / Biso Wilson estimate: 36.6 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 11
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRsym valueDiffraction-ID% possible all
2.2-2.324.40.441.20.44195.6
2.32-2.464.50.3072.50.307195.5
2.46-2.634.50.2133.50.213195.3
2.63-2.844.40.1494.80.149195.1
2.84-3.114.40.10270.102196
3.11-3.484.40.0719.30.071197.6
3.48-4.024.40.0639.70.063199.1
4.02-4.924.30.0757.70.075199
4.92-6.964.20.05510.20.055196.9
6.96-89.444.30.03814.10.038196.8

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Processing

Software
NameVersionClassificationNB
PHENIX1.4_161refinement
REFMACrefinement
PDB_EXTRACT3.005data extraction
MxCuBEdata collection
MOSFLMdata reduction
AMoREphasing
SCALA3.3.1data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1E3M

1e3m


Resolution: 2.2→45.129 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.886 / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.33 / σ(F): 0.01 / Phase error: 25.87 / Stereochemistry target values: ML
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. U VALUES: RESIDUAL ONLY.
RfactorNum. reflection% reflection
Rfree0.2464 5061 5.02 %
Rwork0.1847 --
obs0.1878 100764 92.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.584 Å2 / ksol: 0.353 e/Å3
Displacement parametersBiso mean: 25.726 Å2
Baniso -1Baniso -2Baniso -3
1--4.448 Å20 Å2-0 Å2
2--11.9534 Å20 Å2
3----7.5054 Å2
Refinement stepCycle: LAST / Resolution: 2.2→45.129 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12151 714 27 769 13661
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00713190
X-RAY DIFFRACTIONf_angle_d1.08918006
X-RAY DIFFRACTIONf_dihedral_angle_d17.3415007
X-RAY DIFFRACTIONf_chiral_restr0.0682045
X-RAY DIFFRACTIONf_plane_restr0.0042226
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.27860.34254770.26628606X-RAY DIFFRACTION84
2.2786-2.36990.30964360.23368886X-RAY DIFFRACTION87
2.3699-2.47770.28685120.20839031X-RAY DIFFRACTION89
2.4777-2.60830.30484780.20189311X-RAY DIFFRACTION90
2.6083-2.77170.28094930.20069450X-RAY DIFFRACTION92
2.7717-2.98570.2664890.20329637X-RAY DIFFRACTION93
2.9857-3.28610.2715240.18929873X-RAY DIFFRACTION96
3.2861-3.76140.23825560.171510177X-RAY DIFFRACTION98
3.7614-4.73810.20884990.145510367X-RAY DIFFRACTION99
4.7381-45.13850.19615970.16910365X-RAY DIFFRACTION96
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.33130.2429-0.20920.6926-0.55830.3627-0.05570.00870.0021-0.05380.1768-0.00060.0901-0.0969-0.08730.2247-0.00540.03870.3338-0.02360.130339.364110.192434.2356
23.58170.8363-0.14071.3865-0.23960.65050.0239-0.10240.0245-0.14780.0373-0.19860.0081-0.1349-0.04750.10080.01710.02780.120.00230.105813.94189.21619.9295
31.3864-0.33250.68651.6188-0.91371.3629-0.0322-0.45470.10290.34710.18140.2304-0.1504-0.1349-0.15190.15340.03630.11080.30870.02320.17521.606217.883538.7924
41.3735-0.14330.46941.6676-0.35390.27120.0467-0.07640.00520.18460.18460.1180.2384-0.6975-0.21820.4044-0.03490.00180.47310.04330.094441.279514.604776.2532
50.5275-0.27790.48280.9692-0.67820.6859-0.0295-0.1518-0.0270.00250.18870.2974-0.0071-0.0845-0.1370.0948-0.03460.03050.1997-0.0010.1633-3.522327.281920.1411
61.22040.356-0.5130.335-0.53070.87610.06760.11440.16780.05850.17850.18020.0243-0.17340.05370.1167-0.0157-0.05960.18190.05560.2363-4.350747.4649-3.582
75.49931.57461.96370.62170.57520.87250.9424-1.139-0.71480.5846-0.49830.1450.8068-0.6405-0.37960.7594-0.3349-0.11190.7723-0.02120.518827.078240.876242.5191
80.98820.4236-0.50073.0314-0.62633.4420.1506-0.10960.03310.0506-0.04480.3132-0.1584-0.2991-0.0830.17980.011-0.02440.3057-0.0540.148232.223661.49528.6158
91.01320.15311.17080.6212-0.33412.48060.08740.0460.0224-0.0463-0.0788-0.10070.31780.4247-0.02470.11750.0942-0.01230.2764-0.10130.113149.362550.438916.0977
10-0.00970.2490.19220.4717-0.82181.6309-0.0081-0.0844-0.03260.0572-0.1875-0.03910.03470.21340.15970.25860.04570.02640.62540.00890.24263.996828.085856.9753
111.21240.50241.22460.225-0.09451.61490.16090.15510.0227-0.03390.00690.02610.24920.3977-0.14020.14680.0977-0.03290.2015-0.10820.198437.489151.1746-0.6735
122.29460.49420.03130.81540.4140.7663-0.0410.05230.0662-0.06640.0854-0.07980.0034-0.0892-0.03070.1517-0.0099-0.07430.12510.00840.157912.989147.8521-10.996
130.9139-0.2221.07271.9754-1.20442.01540.0960.1352-0.11750.6928-0.1754-0.37280.05250.20670.05960.29990.0344-0.09290.3612-0.06790.231750.538213.481350.0646
140.8112-0.31110.34221.0382-0.82060.9685-0.2871-0.2996-0.1270.48140.1031-0.0449-0.0551-0.04980.16770.46540.0988-0.00130.4566-0.10210.185148.043115.313752.279
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 2:109)
2X-RAY DIFFRACTION2(chain A and resid 110:259)
3X-RAY DIFFRACTION3(chain A and resid 260:442)
4X-RAY DIFFRACTION4(chain A and resid 443:514)
5X-RAY DIFFRACTION5(chain A and resid 515:697)
6X-RAY DIFFRACTION6(chain A and resid 698:800)
7X-RAY DIFFRACTION7(chain B and resid 13:86)
8X-RAY DIFFRACTION8(chain B and resid 87:260)
9X-RAY DIFFRACTION9(chain B and resid 261:422)
10X-RAY DIFFRACTION10(chain B and resid 423:531)
11X-RAY DIFFRACTION11(chain B and resid 532:659)
12X-RAY DIFFRACTION12(chain B and resid 668:800)
13X-RAY DIFFRACTION13(chain E and resid 1:18)
14X-RAY DIFFRACTION14(chain F and resid 14:30)

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