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- PDB-2zqe: Crystal structure of the Smr domain of Thermus thermophilus MutS2 -

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Basic information

Entry
Database: PDB / ID: 2zqe
TitleCrystal structure of the Smr domain of Thermus thermophilus MutS2
ComponentsMutS2 protein
KeywordsDNA BINDING PROTEIN / alpha/beta / ATP-binding / DNA-binding / Nucleotide-binding
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
Ribosomal Protein S8; Chain: A, domain 1 - #110 / 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 ...Ribosomal Protein S8; Chain: A, domain 1 - #110 / 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 / Ribosomal Protein S8; Chain: A, domain 1 / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsFukui, K. / Kitamura, Y. / Nakagawa, N. / Masui, R. / Kuramitsu, S.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Crystal structure of MutS2 endonuclease domain and the mechanism of homologous recombination suppression
Authors: Fukui, K. / Nakagawa, N. / Kitamura, Y. / Nishida, Y. / Masui, R. / Kuramitsu, S.
History
DepositionAug 8, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 30, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Nov 1, 2023Group: 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MutS2 protein


Theoretical massNumber of molelcules
Total (without water)8,9531
Polymers8,9531
Non-polymers00
Water1,874104
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.813, 54.216, 30.243
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein MutS2 protein


Mass: 8953.281 Da / Num. of mol.: 1 / Fragment: UNP Residue 663-744
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: TTHA1645 / Plasmid: pET-11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5SHT5
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 2.23 Å3/Da / Density % sol: 44.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 3.5
Details: 0.1M Citric acid, 25% PEG 3350, pH 3.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Apr 11, 2008
RadiationMonochromator: transparent diamond double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 9284 / % possible obs: 99.8 % / Redundancy: 6.3 % / Biso Wilson estimate: 11.8 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 36.4
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.137 / Mean I/σ(I) obs: 13.1 / Num. unique all: 58499 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2d9i

2d9i


Resolution: 1.7→7.9 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.934 / SU B: 1.899 / SU ML: 0.066 / Cross valid method: THROUGHOUT / ESU R: 0.114 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22699 443 4.9 %RANDOM
Rwork0.18876 ---
obs0.19074 8597 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.168 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0.04 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.7→7.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms599 0 0 104 703
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.021604
X-RAY DIFFRACTIONr_angle_refined_deg1.0662.005814
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9579
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.45621.92326
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.4415108
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.149159
X-RAY DIFFRACTIONr_chiral_restr0.0660.297
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02448
X-RAY DIFFRACTIONr_nbd_refined0.1980.2260
X-RAY DIFFRACTIONr_nbtor_refined0.3020.2411
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.274
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1160.236
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1720.211
X-RAY DIFFRACTIONr_mcbond_it0.6761.5399
X-RAY DIFFRACTIONr_mcangle_it1.2042621
X-RAY DIFFRACTIONr_scbond_it2.2963212
X-RAY DIFFRACTIONr_scangle_it3.9824.5193
LS refinement shellResolution: 1.702→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 24 -
Rwork0.19 597 -
obs--100 %

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