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- PDB-6oqm: crystal structure of the MSH6 PWWP domain -

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Basic information

Entry
Database: PDB / ID: 6oqm
Titlecrystal structure of the MSH6 PWWP domain
ComponentsDNA mismatch repair protein Msh6
KeywordsDNA BINDING PROTEIN / PWWP domain / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


MutSalpha complex / Defective Mismatch Repair Associated With MSH2 / Defective Mismatch Repair Associated With MSH6 / guanine/thymine mispair binding / somatic recombination of immunoglobulin gene segments / positive regulation of helicase activity / meiotic mismatch repair / mismatched DNA binding / negative regulation of DNA recombination / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) ...MutSalpha complex / Defective Mismatch Repair Associated With MSH2 / Defective Mismatch Repair Associated With MSH6 / guanine/thymine mispair binding / somatic recombination of immunoglobulin gene segments / positive regulation of helicase activity / meiotic mismatch repair / mismatched DNA binding / negative regulation of DNA recombination / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / isotype switching / ATP-dependent DNA damage sensor activity / mismatch repair / somatic hypermutation of immunoglobulin genes / ATP-dependent activity, acting on DNA / response to UV / methylated histone binding / intrinsic apoptotic signaling pathway / determination of adult lifespan / intrinsic apoptotic signaling pathway in response to DNA damage / spermatogenesis / damaged DNA binding / DNA repair / intracellular membrane-bounded organelle / chromatin binding / chromatin / Golgi apparatus / enzyme binding / nucleoplasm / ATP binding / nucleus / cytosol
Similarity search - Function
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 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 / domain with conserved PWWP motif / PWWP domain / PWWP domain profile. / PWWP domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
DNA mismatch repair protein Msh6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsQin, S. / Tempel, W. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Structural Genomics Consortium / Structural Genomics Consortium (SGC)
CitationJournal: To Be Published
Title: crystal structure of the MSH6 PWWP domain
Authors: Qin, S. / Tempel, W. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Structural Genomics Consortium
History
DepositionApr 26, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA mismatch repair protein Msh6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,55410
Polymers15,1451
Non-polymers4099
Water362
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.421, 56.421, 176.291
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-202-

MG

21A-205-

SO4

31A-205-

SO4

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Components

#1: Protein DNA mismatch repair protein Msh6 / / hMSH6 / G/T mismatch-binding protein / GTMBP / MutS protein homolog 6 / MutS-alpha 160 kDa subunit / p160


Mass: 15145.189 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MSH6, GTBP / Plasmid: pET28-MHL / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): -V2R-pRARE2 / References: UniProt: P52701
#2: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 4 / Source method: obtained synthetically
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 1.78 Å3/Da / Density % sol: 31.01 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 1.6 M ammonium sulfate, 0.1 M sodium cacodylate pH 5.5, 0.01 M magnesium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 20, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.2→47.09 Å / Num. obs: 5806 / % possible obs: 99.9 % / Redundancy: 10.6 % / CC1/2: 1 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.018 / Rrim(I) all: 0.059 / Net I/σ(I): 25.6 / Num. measured all: 61628 / Scaling rejects: 8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.2-2.2710.71.3254970.7620.4231.39298.8
9.06-47.097.80.0221060.9990.0080.02499.3

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.24data extraction
MR-Rosettaphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 5vc8

5vc8


Resolution: 2.2→29.382 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 0.27 / Phase error: 34.54
RfactorNum. reflection% reflection
Rfree0.2698 1030 9.68 %
Rwork0.2167 --
obs0.2217 10645 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 106.67 Å2 / Biso mean: 56.6048 Å2 / Biso min: 37.51 Å2
Refinement stepCycle: final / Resolution: 2.2→29.382 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms775 0 25 2 802
Biso mean--75.64 45.14 -
Num. residues----100
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.2001-2.31610.37531520.358413791531
2.3161-2.46110.36131520.305413611513
2.4611-2.6510.40291770.295513431520
2.651-2.91760.36871450.239713811526
2.9176-3.33930.35771230.249113841507
3.3393-4.20520.22891390.185113811520
4.2052-29.38440.21111420.188913861528

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