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- PDB-7vuf: Crystal Structure of the core region of Thermus thermophilus MutS2. -

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Basic information

Entry
Database: PDB / ID: 7vuf
TitleCrystal Structure of the core region of Thermus thermophilus MutS2.
ComponentsEndonuclease MutS2
KeywordsDNA BINDING PROTEIN / ATPase / hydrolase
Function / homology
Function and homology information


Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 3'-phosphomonoesters / mismatched DNA binding / negative regulation of DNA recombination / ATP-dependent DNA damage sensor activity / ribosomal large subunit binding / mismatch repair / rescue of stalled ribosome / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / endonuclease activity / rRNA binding ...Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 3'-phosphomonoesters / mismatched DNA binding / negative regulation of DNA recombination / ATP-dependent DNA damage sensor activity / ribosomal large subunit binding / mismatch repair / rescue of stalled ribosome / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / endonuclease activity / rRNA binding / ATP hydrolysis activity / ATP binding
Similarity search - Function
Endonuclease MutS2 / MutS2 and Smr-associated SH3 domain / MutS2 and Smr-associated SH3 domain / Smr domain / Small MutS-related domain / Smr domain superfamily / Smr domain / Smr domain profile. / DNA mismatch repair MutS family / DNA mismatch repair protein MutS, C-terminal ...Endonuclease MutS2 / MutS2 and Smr-associated SH3 domain / MutS2 and Smr-associated SH3 domain / Smr domain / Small MutS-related domain / Smr domain superfamily / Smr domain / Smr domain profile. / 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 / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Endonuclease MutS2
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.11 Å
AuthorsFukui, K. / Yano, T.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Structure / Year: 2022
Title: Structural and functional insights into the mechanism by which MutS2 recognizes a DNA junction.
Authors: Fukui, K. / Inoue, M. / Murakawa, T. / Baba, S. / Kumasaka, T. / Yano, T.
History
DepositionNov 2, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 6, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2022Group: Database references / Category: citation / citation_author
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.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Endonuclease MutS2
A: Endonuclease MutS2
C: Endonuclease MutS2
D: Endonuclease MutS2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)217,48912
Polymers216,7214
Non-polymers7678
Water1,928107
1
B: Endonuclease MutS2
hetero molecules

C: Endonuclease MutS2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,9168
Polymers108,3612
Non-polymers5556
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_545x,y-1,z1
Buried area3910 Å2
ΔGint-30 kcal/mol
Surface area43730 Å2
MethodPISA
2
A: Endonuclease MutS2
D: Endonuclease MutS2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,5734
Polymers108,3612
Non-polymers2122
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3650 Å2
ΔGint-31 kcal/mol
Surface area43060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.485, 114.207, 292.879
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein
Endonuclease MutS2


Mass: 54180.355 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: No clear electron density was observed for the residues 166-172, 187-196, 361-367, and 488 of the chain A, 1, 167-171, 187-196, 361-367, and 487-488 of the chain B, 164-170, 361-365, 467, ...Details: No clear electron density was observed for the residues 166-172, 187-196, 361-367, and 488 of the chain A, 1, 167-171, 187-196, 361-367, and 487-488 of the chain B, 164-170, 361-365, 467, 487-488 of the chain C, 1, 167-173, 192-195, 211-218, 360-364 of the chain D.
Source: (gene. exp.) Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8) (bacteria)
Strain: ATCC 27634 / DSM 579 / HB8 / Gene: mutS2, TTHA1645 / Plasmid: pET11a / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2
References: UniProt: Q5SHT5, Hydrolases; Acting on ester bonds
#2: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.69 Å3/Da / Density % sol: 66.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 25 mM HEPES-NaOH (pH 7.0), 100 mM potassium chloride, 12.5 mM magnesium sulfate, 10% (v/v) PEG 200

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Oct 26, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.98→50 Å / Num. obs: 53869 / % possible obs: 99.8 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.271 / Rpim(I) all: 0.117 / Rrim(I) all: 0.296 / Χ2: 2.009 / Net I/σ(I): 10.13
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.98-3.146.51.671111110.4990.711.8181.246100
3.14-3.396.40.899111360.7120.3830.9791.346100
3.39-3.736.40.515111430.8750.2210.5611.654100
3.73-4.266.40.319112300.9190.1380.3482.46100
4.26-5.376.30.217112980.9260.0950.2373.908100
5.37-106.30.166117110.9460.070.18114.51399.8

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Processing

Software
NameVersionClassification
PHENIX1.19.2refinement
HKL-2000data reduction
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
PHASERphasing
PHENIX1.19.2model building
Coot0.7.2model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.11→40.89 Å / SU ML: 0.4461 / Cross valid method: FREE R-VALUE / σ(F): 0.13 / Phase error: 27.436
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2785 2586 4.8 %
Rwork0.2248 51283 -
obs0.2274 53869 94.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 52.5 Å2
Refinement stepCycle: LAST / Resolution: 3.11→40.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14285 0 50 107 14442
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001814525
X-RAY DIFFRACTIONf_angle_d0.503519607
X-RAY DIFFRACTIONf_chiral_restr0.03612276
X-RAY DIFFRACTIONf_plane_restr0.00362568
X-RAY DIFFRACTIONf_dihedral_angle_d13.99223701
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.11-3.170.40231150.3112499X-RAY DIFFRACTION83.41
3.17-3.230.35611270.30032559X-RAY DIFFRACTION85.95
3.23-3.30.39131410.28892640X-RAY DIFFRACTION89.34
3.3-3.380.37871260.27312766X-RAY DIFFRACTION91.06
3.38-3.470.32821380.25762752X-RAY DIFFRACTION91.95
3.47-3.560.33711390.25222709X-RAY DIFFRACTION91.72
3.56-3.660.25191540.23012824X-RAY DIFFRACTION94
3.66-3.780.29691440.22972826X-RAY DIFFRACTION93.75
3.78-3.920.26931360.21712837X-RAY DIFFRACTION94.65
3.92-4.070.24881470.21162864X-RAY DIFFRACTION94.66
4.07-4.260.23461490.19712882X-RAY DIFFRACTION95.95
4.26-4.480.27951540.19062916X-RAY DIFFRACTION96.66
4.48-4.760.24871320.19412954X-RAY DIFFRACTION96.83
4.76-5.130.28891480.19982946X-RAY DIFFRACTION97.48
5.13-5.650.25151690.22792954X-RAY DIFFRACTION97.56
5.65-6.460.2931490.25143021X-RAY DIFFRACTION98.17
6.46-8.130.26031710.21433092X-RAY DIFFRACTION99.6
8.13-100.22421470.20143242X-RAY DIFFRACTION99.24
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)
11.12378732089-0.1611321022430.5917481926280.151216459652-0.1253435857350.558885481738-0.0571225634287-0.1358865993660.138806570118-0.0794845189133-0.0108556719864-0.0915441463243-0.0220891301551-0.1116889991180.07272602599630.374336356414-0.02307236513640.03084486809980.299201155789-0.09183213024950.396178048841-0.613484000106-13.8303376579-40.1621527154
21.14438087159-0.1230833142910.3884728928770.171719693455-0.1779177966970.2282794931460.0506299779061-0.0877007423893-0.149818121956-0.00062486390312-0.0109679541056-0.0208997353785-0.0283784153164-0.0196663571264-0.03024098469150.3791650106910.001652993294610.03300748497810.309444488069-0.1134567565330.318950119994-29.395196803815.0533148506-20.7364899565
31.22888052735-1.020383390220.5905527027080.957470581246-0.3967599659760.2871279790240.06791246606120.0106436305151-0.0395935883882-0.0702796830793-0.05999697999650.08672502091680.053357924854-0.0076426082952-0.0001652726633190.332638164363-0.03810874377730.04906184759750.3990173863240.007999568967510.298715360864-14.443367292653.8405114075-60.0481900348
40.862064456046-0.5735303415880.1663098614030.495317195662-0.1788364134520.02012897741880.01307690223360.1213426853480.127568097836-0.0483259295661-0.0570829127937-0.1488813724320.0500982129355-0.01869162016490.03430962765610.45613169015-0.02473163291570.02390159843030.397616307546-0.09202215001960.375980663682-10.016380643463.0887819961-9.91392433066
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain B and resseq 2:487)BA2 - 4871 - 471
22(chain A and resseq 1:485)AB1 - 4851 - 461
33(chain C and resseq 1:486)CC1 - 4861 - 473
44(chain D and resseq 2:488)DD2 - 4881 - 463

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