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- PDB-7vuk: Crystal Structure of the core region of Thermus thermophilus MutS... -

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Basic information

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


mismatched DNA binding / negative regulation of DNA recombination / mismatch repair / endonuclease activity / Hydrolases; Acting on ester bonds / ATP hydrolysis activity / ATP binding
Similarity search - Function
MutS2 and Smr-associated SH3 domain / MutS2 and Smr-associated SH3 domain / Endonuclease MutS2 / Smr domain superfamily / Smr domain / Small MutS-related domain / Smr domain / Smr domain profile. / DNA mismatch repair protein MutS, C-terminal / DNA mismatch repair protein MutS, core ...MutS2 and Smr-associated SH3 domain / MutS2 and Smr-associated SH3 domain / Endonuclease MutS2 / Smr domain superfamily / Smr domain / Small MutS-related domain / Smr domain / Smr domain profile. / 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 / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / DI(HYDROXYETHYL)ETHER / Endonuclease MutS2
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.38 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 1.2Nov 29, 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: Endonuclease MutS2
B: Endonuclease MutS2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,68830
Polymers108,3612
Non-polymers2,32728
Water1,06359
1
A: Endonuclease MutS2
hetero molecules

B: Endonuclease MutS2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,68830
Polymers108,3612
Non-polymers2,32728
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_455-x-1/2,y+1/2,-z+1/41
Buried area9040 Å2
ΔGint-169 kcal/mol
Surface area41140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.654, 133.654, 197.461
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 1 through 18 or (resid 19...
d_2ens_1(chain "B" and (resid 1 or (resid 2 and (name...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1METASPA1 - 300
d_12ens_1GLNGLUA302 - 421
d_21ens_1METLEUC1 - 156
d_22ens_1LYSASPC205 - 434
d_23ens_1ALAPROC437 - 449
d_24ens_1SERGLUC452 - 472

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Endonuclease MutS2


Mass: 54180.355 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: No clear electron density was observed for the residues 157-216, 361-363, 451-452, and 466-467 of the chain A, and the residues 165-171, 201-205, and 361-364 of the chain B.
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

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Non-polymers , 6 types, 87 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


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


Mass: 18.015 Da / Num. of mol.: 59 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 4.07 Å3/Da / Density % sol: 69.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 50 mM Tris-HCl (pH 8.5), 2.5 mM magnesium sulfate, 1.45 M 1,6-hexanediol, 2.5 mM ADP

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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: May 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.38→50 Å / Num. obs: 30328 / % possible obs: 100 % / Redundancy: 12.2 % / Rmerge(I) obs: 0.315 / Rpim(I) all: 0.154 / Rrim(I) all: 0.411 / Χ2: 1.354 / Net I/σ(I): 6.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.38-3.4511.63.22615080.4320.973.3721.247100
3.45-3.5211.62.79314860.4380.842.921.274100
3.52-3.611.82.8114750.5120.8412.9351.271100
3.6-3.6911.91.29915030.5810.3861.3561.43100
3.69-3.79121.41814870.7430.421.481.352100
3.79-3.9112.21.08514960.7760.3191.1311.355100
3.91-4.0312.10.88815130.8270.2620.9271.339100
4.03-4.1812.30.70914920.9060.2080.7391.379100
4.18-4.3412.40.53715090.950.1560.561.446100
4.34-4.5412.50.4914970.9610.1420.5111.47100
4.54-4.7812.50.44415270.9670.1290.4631.387100
4.78-5.0812.80.44915200.9670.1290.4681.323100
5.08-5.4713.10.51715240.9590.1470.5381.289100
5.47-6.0213.40.46915310.9650.1320.4871.32100
6.02-6.8913.50.3115570.9810.0870.3221.355100
6.89-8.6713.10.13715790.9970.0390.1421.412100
8.67-5011.50.07216900.9980.0220.0751.54599.2

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Processing

Software
NameVersionClassification
PHENIX1.19.2refinement
HKL-2000data reduction
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
PHENIX1.19.2phasing
PHENIX1.19.2model building
Coot0.7.1model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7VUF

7vuf


Resolution: 3.38→49.37 Å / SU ML: 0.5155 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.855
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2724 1269 4.94 %
Rwork0.2669 24431 -
obs0.2671 25700 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 62.5 Å2
Refinement stepCycle: LAST / Resolution: 3.38→49.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6397 0 140 59 6596
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00326607
X-RAY DIFFRACTIONf_angle_d0.698969
X-RAY DIFFRACTIONf_chiral_restr0.04081074
X-RAY DIFFRACTIONf_plane_restr0.00441162
X-RAY DIFFRACTIONf_dihedral_angle_d17.79571479
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 2.04433930451 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.38-3.520.41371340.38762674X-RAY DIFFRACTION99.79
3.52-3.680.30351330.32492643X-RAY DIFFRACTION99.86
3.68-3.870.32431370.30352665X-RAY DIFFRACTION100
3.87-4.110.25661520.25012680X-RAY DIFFRACTION100
4.11-4.430.23771180.23772711X-RAY DIFFRACTION100
4.43-4.870.26721630.24832669X-RAY DIFFRACTION100
4.87-5.580.32831240.27272759X-RAY DIFFRACTION100
5.58-7.020.25961540.25722743X-RAY DIFFRACTION99.97
7.03-49.370.22261540.2222887X-RAY DIFFRACTION99.35
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)
10.0909393183218-0.03710384986880.01214316384830.01988131066540.03861593190510.1790590619990.07708378037930.0810024237388-0.05485673318660.1381255684490.0667154426877-0.08748265306970.0329926783998-0.0436496509366-0.0916161370940.4047750729450.08802741960880.02112530816120.692952468591-0.06785892123570.497921182363-27.9131.3341.477
21.52958394813-0.02608309123480.7219016853590.446281008238-0.3391675463831.142056700430.05753300972570.118107861751-0.364333298488-0.3996032471880.2503588092470.2336764550840.107431033247-0.240692257937-0.2237907232450.746594794606-0.0453133873152-0.1431536437080.5564674206210.08422635526780.523618924087-29.260496477953.2462961647-6.6934026698
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth seq-ID: 1 - 488

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDLabel seq-ID
11(chain B and resseq 1:488)BC1 - 486
22(chain A and resseq 1:488)AA1 - 419

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