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- PDB-6i5f: Crystal structure of DNA-free E.coli MutS P839E dimer mutant -

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Basic information

Entry
Database: PDB / ID: 6i5f
TitleCrystal structure of DNA-free E.coli MutS P839E dimer mutant
ComponentsDNA mismatch repair protein MutS
KeywordsDNA BINDING PROTEIN / MutS / DNA mismatch repair / helix folding / ABC-ATPase / coiled coil / helix kink / apo-MutS
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 / 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
ADENOSINE-5'-DIPHOSPHATE / DNA mismatch repair protein MutS
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsBhairosing-Kok, D. / Groothuizen, F.S. / Fish, A. / Dharadhar, S. / Winterwerp, H.H.K. / Sixma, T.K.
Funding support Netherlands, 4items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific ResearchTOP 714.016.002 Netherlands
Netherlands Organisation for Scientific ResearchECHO 711.011.011 Netherlands
Netherlands Organisation for Scientific ResearchCGC.nl Netherlands
European UnionMM2M (FP7)
CitationJournal: Nucleic Acids Res. / Year: 2019
Title: Sharp kinking of a coiled-coil in MutS allows DNA binding and release.
Authors: Bhairosing-Kok, D. / Groothuizen, F.S. / Fish, A. / Dharadhar, S. / Winterwerp, H.H.K. / Sixma, T.K.
History
DepositionNov 13, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 14, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)193,69226
Polymers190,7762
Non-polymers2,91624
Water2,522140
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12060 Å2
ΔGint-195 kcal/mol
Surface area67070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.375, 113.525, 158.904
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein DNA mismatch repair protein MutS /


Mass: 95387.789 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: mutS, fdv, b2733, JW2703 / Production host: Escherichia coli (E. coli) / References: UniProt: P23909
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


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


Mass: 18.015 Da / Num. of mol.: 140 / 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: 3.14 Å3/Da / Density % sol: 60.51 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1 M Hepes 7.0 7 % Dioxone 1.4 M Ammonium Sulfate

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 16, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.6→80.22 Å / Num. obs: 62205 / % possible obs: 98.1 % / Redundancy: 4.1 % / Biso Wilson estimate: 38.87 Å2 / CC1/2: 0.957 / Rmerge(I) obs: 0.299 / Rpim(I) all: 0.167 / Rrim(I) all: 0.344 / Net I/σ(I): 4.6 / Num. measured all: 253695 / Scaling rejects: 79
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.6-2.6741.19443810.110.6731.37494.9
11.63-80.223.70.0737310.990.0430.08594.3

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Processing

Software
NameVersionClassification
BUSTERrefinement
MOSFLM6.2.6data reduction
Aimless0.3.11data scaling
PHASER2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WB9

1wb9


Resolution: 2.6→71.61 Å / Cor.coef. Fo:Fc: 0.902 / Cor.coef. Fo:Fc free: 0.855 / SU R Cruickshank DPI: 0.54 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.52 / SU Rfree Blow DPI: 0.294 / SU Rfree Cruickshank DPI: 0.301
Details: Residues 12-80 (mismatch binding domain) in chain A and residues 442-503 (clamp domain) in chain B are are likely flexible They were placed in the structure using conserved fold of the ...Details: Residues 12-80 (mismatch binding domain) in chain A and residues 442-503 (clamp domain) in chain B are are likely flexible They were placed in the structure using conserved fold of the mismatch binding domain and clamp domain, respectively
RfactorNum. reflection% reflectionSelection details
Rfree0.257 3051 4.91 %RANDOM
Rwork0.206 ---
obs0.209 62187 97.6 %-
Displacement parametersBiso max: 184.83 Å2 / Biso mean: 59.92 Å2 / Biso min: 7.11 Å2
Baniso -1Baniso -2Baniso -3
1--3.2441 Å20 Å20 Å2
2---2.1574 Å20 Å2
3---5.4015 Å2
Refine analyzeLuzzati coordinate error obs: 0.4 Å
Refinement stepCycle: final / Resolution: 2.6→71.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12134 0 177 140 12451
Biso mean--60.46 26.01 -
Num. residues----1537
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d4496SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes2149HARMONIC5
X-RAY DIFFRACTIONt_it12499HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1630SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact14663SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d12499HARMONIC20.011
X-RAY DIFFRACTIONt_angle_deg16909HARMONIC21.27
X-RAY DIFFRACTIONt_omega_torsion2.87
X-RAY DIFFRACTIONt_other_torsion21.3
LS refinement shellResolution: 2.6→2.67 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2815 214 4.89 %
Rwork0.251 4160 -
all0.2525 4374 -
obs--94.37 %
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)
10.01140.0002-0.01460.0027-0.03490.01630-0.00010.00030.0002-0.00040.00070-0.00030.0005-0.0001-0.00190.00120.00090.00290.0005-12.6104-9.728132.2641
21.10710.1289-0.72620.1245-0.25070.12480.00250.0108-0.0076-0.00560.00560.00720.016-0.0044-0.0081-0.01380.01440.01230.00770.020.0065.5296-0.1359.6551
30.12420.0974-0.05680.0786-0.04540.00770.0001-0.00080.00150.0016-0.00220.00070.00140.00050.0021-0.009-0.00560.01070.0038-0.00150.0071-53.905220.35889.4219
40.1537-0.24650.08530.0566-0.26420.21440.0025-0.00390.0103-0.0027-0.00620.0074-0.00370.02160.0037-0.00940.01040.01530.01410.026-0.009734.63784.410117.334
50-0.08720.18870.10910.01750.0941-0.0004-0.0011-0.0014-0.0009-0.00060.0009-0.00050.0010.00110.0040.0088-0.0111-0.00410.0049-0.0041-6.004423.392534.0501
60.2775-0.281.30430-0.47440.32650.0031-0.00870.0116-0.00770.0109-0.0023-0.0055-0.0106-0.01390.00780.0316-0.04010.00190.006-0.01288.23428.418157.4773
70.028-0.04840.00190.01340.00560.006500.0002-0.00020.00020.0001-0.00010.00010-0.000100.0013-0.00060.00070.00010.0009-37.310617.104732.8725
80-0.32250.00480-0.26950.98980-0.0070.0065-0.0105-0.0088-0.0060.00580.0040.00890.01780.0151-0.0085-0.0008-0.0082-0.023232.8888-7.311649.7737
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|12 - A|94 A|109 - A|112 }A12 - 94
2X-RAY DIFFRACTION1{ A|12 - A|94 A|109 - A|112 }A109 - 112
3X-RAY DIFFRACTION2{ A|113 - A|441 }A113 - 441
4X-RAY DIFFRACTION3{ A|442 - A|515 }A442 - 515
5X-RAY DIFFRACTION4{ A|516 - A|657 A|668 - A|750 A|755 - A|799 }A516 - 657
6X-RAY DIFFRACTION4{ A|516 - A|657 A|668 - A|750 A|755 - A|799 }A668 - 750
7X-RAY DIFFRACTION4{ A|516 - A|657 A|668 - A|750 A|755 - A|799 }A755 - 799
8X-RAY DIFFRACTION5{ B|6 - B|94 B|104 - B|112 }B6 - 94
9X-RAY DIFFRACTION5{ B|6 - B|94 B|104 - B|112 }B104 - 112
10X-RAY DIFFRACTION6{ B|113 - B|441 }B113 - 441
11X-RAY DIFFRACTION7{ B|442 - B|515 }B442 - 515
12X-RAY DIFFRACTION8{ B|516 - B|658 B|667 - B|799 }B516 - 658
13X-RAY DIFFRACTION8{ B|516 - B|658 B|667 - B|799 }B667 - 799

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