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- PDB-6sns: DNA mismatch repair proteins MLH1 and MLH3 -

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Basic information

Entry
Database: PDB / ID: 6sns
TitleDNA mismatch repair proteins MLH1 and MLH3
Components
  • DNA mismatch repair protein MLH1
  • DNA mismatch repair protein MLH3
KeywordsRECOMBINATION / RESOLVASE / MMR / DNA REPAIR / MEIOSIS
Function / homology
Function and homology information


meiotic heteroduplex formation / MutLbeta complex / MutLgamma complex / MutLalpha complex / mismatch repair complex / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / meiotic mismatch repair / mismatched DNA binding / reciprocal meiotic recombination / ATP-dependent DNA damage sensor activity ...meiotic heteroduplex formation / MutLbeta complex / MutLgamma complex / MutLalpha complex / mismatch repair complex / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / meiotic mismatch repair / mismatched DNA binding / reciprocal meiotic recombination / ATP-dependent DNA damage sensor activity / mismatch repair / ATP hydrolysis activity / mitochondrion / ATP binding / nucleus / cytoplasm
Similarity search - Function
DNA mismatch repair protein Mlh1, C-terminal / DNA mismatch repair protein Mlh1 C-terminus / MutL C terminal dimerisation domain / MutL, C-terminal, dimerisation / MutL, C-terminal domain superfamily / MutL, C-terminal domain, dimerisation subdomain / MutL C terminal dimerisation domain / DNA mismatch repair protein family, N-terminal / DNA mismatch repair protein, S5 domain 2-like / DNA mismatch repair, conserved site ...DNA mismatch repair protein Mlh1, C-terminal / DNA mismatch repair protein Mlh1 C-terminus / MutL C terminal dimerisation domain / MutL, C-terminal, dimerisation / MutL, C-terminal domain superfamily / MutL, C-terminal domain, dimerisation subdomain / MutL C terminal dimerisation domain / DNA mismatch repair protein family, N-terminal / DNA mismatch repair protein, S5 domain 2-like / DNA mismatch repair, conserved site / DNA mismatch repair protein MutL/Mlh/Pms / DNA mismatch repair protein, C-terminal domain / DNA mismatch repair proteins mutL / hexB / PMS1 signature. / DNA mismatch repair protein, C-terminal domain / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold
Similarity search - Domain/homology
DNA mismatch repair protein MLH1 / DNA mismatch repair protein MLH3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsDai, J. / Chervy, P. / Legrand, P. / Ropars, V. / Charbonnier, J.B.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyANR-Resolve France
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2021
Title: Molecular basis of the dual role of the Mlh1-Mlh3 endonuclease in MMR and in meiotic crossover formation.
Authors: Dai, J. / Sanchez, A. / Adam, C. / Ranjha, L. / Reginato, G. / Chervy, P. / Tellier-Lebegue, C. / Andreani, J. / Guerois, R. / Ropars, V. / Le Du, M.H. / Maloisel, L. / Martini, E. / ...Authors: Dai, J. / Sanchez, A. / Adam, C. / Ranjha, L. / Reginato, G. / Chervy, P. / Tellier-Lebegue, C. / Andreani, J. / Guerois, R. / Ropars, V. / Le Du, M.H. / Maloisel, L. / Martini, E. / Legrand, P. / Thureau, A. / Cejka, P. / Borde, V. / Charbonnier, J.B.
History
DepositionAug 27, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 19, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 1, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 24, 2024Group: 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 MLH1
B: DNA mismatch repair protein MLH3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,5973
Polymers58,5312
Non-polymers651
Water63135
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, two-hybrid, genetic
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2170 Å2
ΔGint-57 kcal/mol
Surface area25410 Å2
Unit cell
Length a, b, c (Å)91.860, 103.090, 135.140
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

#1: Protein DNA mismatch repair protein MLH1 / MutL protein homolog 1 / Post meiotic segregation protein 2


Mass: 30764.279 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: MLH1, PMS2, YMR167W, YM8520.16 / Production host: Escherichia coli (E. coli) / References: UniProt: P38920
#2: Protein DNA mismatch repair protein MLH3 / MutL protein homolog 3


Mass: 27767.180 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: MLH3, YPL164C, P2550 / Production host: Escherichia coli (E. coli) / References: UniProt: Q12083
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.92 Å3/Da / Density % sol: 57.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6 / Details: PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9786 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 13501 / % possible obs: 95 % / Redundancy: 6.5 % / Biso Wilson estimate: 124 Å2 / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.022 / Rrim(I) all: 0.056 / Net I/σ(I): 16
Reflection shellResolution: 2.6→2.78 Å / Rmerge(I) obs: 1.47 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 675 / Rpim(I) all: 0.613 / Rrim(I) all: 1.6

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4E4W

4e4w


Resolution: 2.6→48.13 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.939 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.386
RfactorNum. reflection% reflectionSelection details
Rfree0.246 683 5.13 %RANDOM
Rwork0.215 ---
obs0.217 13316 66.4 %-
Displacement parametersBiso max: 253.12 Å2 / Biso mean: 114.53 Å2 / Biso min: 42.91 Å2
Baniso -1Baniso -2Baniso -3
1--1.1822 Å20 Å20 Å2
2--2.5221 Å20 Å2
3----1.3399 Å2
Refine analyzeLuzzati coordinate error obs: 0.41 Å
Refinement stepCycle: final / Resolution: 2.6→48.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3849 0 1 35 3885
Biso mean--87.96 68.68 -
Num. residues----473
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1409SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes649HARMONIC5
X-RAY DIFFRACTIONt_it3920HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion508SEMIHARMONIC5
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_contact4302SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3920HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg5288HARMONIC21.01
X-RAY DIFFRACTIONt_omega_torsion2.24
X-RAY DIFFRACTIONt_other_torsion19.98
LS refinement shellResolution: 2.6→2.72 Å / Rfactor Rfree error: 0 / Total num. of bins used: 34
RfactorNum. reflection% reflection
Rfree0.3138 22 5.61 %
Rwork0.2272 370 -
all0.2321 392 -
obs--15.69 %
Refinement TLS params.Method: refined / Origin x: 28.7416 Å / Origin y: 15.7293 Å / Origin z: 21.0622 Å
111213212223313233
T-0.2174 Å20.0954 Å2-0.0454 Å2--0.0234 Å2-0.0395 Å2--0.0662 Å2
L1.2853 °2-0.5836 °2-2.1952 °2-1.8401 °20.8179 °2--8.124 °2
S-0.2387 Å °-0.3022 Å °0.1825 Å °0.3965 Å °0.1372 Å °0.212 Å °-0.0521 Å °0.3942 Å °0.1015 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|505 - A|769 A|801 - A|810 B|901 - B|925 B|486 - B|712 B|801 - B|801 }A505 - 769
2X-RAY DIFFRACTION1{ A|505 - A|769 A|801 - A|810 B|901 - B|925 B|486 - B|712 B|801 - B|801 }A801 - 810
3X-RAY DIFFRACTION1{ A|505 - A|769 A|801 - A|810 B|901 - B|925 B|486 - B|712 B|801 - B|801 }B901 - 925
4X-RAY DIFFRACTION1{ A|505 - A|769 A|801 - A|810 B|901 - B|925 B|486 - B|712 B|801 - B|801 }B486 - 712
5X-RAY DIFFRACTION1{ A|505 - A|769 A|801 - A|810 B|901 - B|925 B|486 - B|712 B|801 - B|801 }B801

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