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- PDB-2wtu: Crystal structure of Escherichia coli MutS in complex with a 16 b... -

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Basic information

Entry
Database: PDB / ID: 2wtu
TitleCrystal structure of Escherichia coli MutS in complex with a 16 basepair oligo containing an A.A mismatch.
Components
  • (DNA) x 2
  • DNA MISMATCH REPAIR PROTEIN MUTS
KeywordsDNA BINDING PROTEIN/DNA / DNA BINDING PROTEIN-DNA COMPLEX / DNA DAMAGE / DNA REPAIR / NUCLEOTIDE-BINDING
Function / homology
Function and homology information


adenine/cytosine mispair binding / MutS complex / mismatch repair complex / regulation of DNA recombination / mismatched DNA binding / DNA binding, bending / ATP-dependent DNA damage sensor activity / mismatch repair / ADP binding / damaged DNA binding ...adenine/cytosine mispair binding / MutS complex / mismatch repair complex / regulation of DNA recombination / mismatched DNA binding / DNA binding, bending / ATP-dependent DNA damage sensor activity / mismatch repair / ADP binding / damaged DNA binding / DNA damage response / ATP hydrolysis activity / ATP binding / identical protein binding / cytosol
Similarity search - Function
MutS, connector domain / DNA repair protein MutS, domain I / MutS, DNA mismatch repair protein; Chain A, domain 3 / MutS, DNA mismatch repair protein; Chain A, domain 3 - #10 / DNA mismatch repair protein MutS / 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 / DNA repair protein MutS, domain I / MutS, DNA mismatch repair protein; Chain A, domain 3 / MutS, DNA mismatch repair protein; Chain A, domain 3 - #10 / DNA mismatch repair protein MutS / 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 / MutS, DNA mismatch repair protein, domain I / Nucleotidyltransferase; domain 5 / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / DNA / DNA (> 10) / DNA mismatch repair protein MutS
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsNatrajan, G. / Lebbink, J.H. / Reumer, A. / Fish, A. / Winterwerp, H.H. / Sixma, T.K.
CitationJournal: J. Biol. Chem. / Year: 2010
Title: Magnesium coordination controls the molecular switch function of DNA mismatch repair protein MutS.
Authors: Lebbink, J.H. / Fish, A. / Reumer, A. / Natrajan, G. / Winterwerp, H.H. / Sixma, T.K.
History
DepositionSep 22, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 9, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 7, 2018Group: Database references / Source and taxonomy / Category: citation / entity_src_gen / pdbx_entity_src_syn
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA MISMATCH REPAIR PROTEIN MUTS
B: DNA MISMATCH REPAIR PROTEIN MUTS
E: DNA
F: DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)189,5508
Polymers189,0164
Non-polymers5344
Water73941
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11590 Å2
ΔGint-94.1 kcal/mol
Surface area70110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.105, 137.890, 161.446
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein DNA MISMATCH REPAIR PROTEIN MUTS / / MUTS


Mass: 89604.359 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-800
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PMQ372 / Production host: Escherichia coli B (bacteria) / Strain (production host): B834 / Variant (production host): pLysS / References: UniProt: P23909

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DNA chain , 2 types, 2 molecules EF

#2: DNA chain DNA /


Mass: 4877.183 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: THIS IS A CHEMICALLY SYNTHESIZED OLIGONUCLEOTIDE. / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA /


Mass: 4930.189 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: THIS IS A CHEMICALLY SYNTHESIZED OLIGONUCLEOTIDE. / Source: (synth.) synthetic construct (others)

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Non-polymers , 3 types, 45 molecules

#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 41 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE CRYSTALLIZED CONSTRUCT HAD ONLY THE FIRST 800 RESIDUES OF P23909

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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: 2.82 Å3/Da / Density % sol: 56.36 % / Description: NONE
Crystal growpH: 7.5
Details: 18% PEG 3350, 100 MM SODIUM CITRATE, 100 MM BIS TRIS PROPANE PH 7.5, 5 MM MGCL2, 100 MICROM ADP.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.93
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 15, 2004 / Details: TOROIDAL MIRRORS
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 3.4→50 Å / Num. obs: 28641 / % possible obs: 99.8 % / Observed criterion σ(I): 1.1 / Redundancy: 7.2 % / Biso Wilson estimate: 72.1 Å2 / Rmerge(I) obs: 0.15 / Net I/σ(I): 13.6
Reflection shellResolution: 3.4→3.58 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 4.3 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.5.0072refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OH6

1oh6


Resolution: 3.4→50 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.88 / SU B: 30.691 / SU ML: 0.491 / Cross valid method: THROUGHOUT / ESU R Free: 0.624 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. MISSING RESIDUES ARE DUE TO LACK OF VISIBLE ELECTRON DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.26303 1446 5.1 %RANDOM
Rwork0.20317 ---
obs0.20625 27154 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 52.791 Å2
Baniso -1Baniso -2Baniso -3
1--5.28 Å20 Å20 Å2
2---2.25 Å20 Å2
3---7.53 Å2
Refinement stepCycle: LAST / Resolution: 3.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12028 654 30 41 12753
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.02212990
X-RAY DIFFRACTIONr_bond_other_d0.0010.028714
X-RAY DIFFRACTIONr_angle_refined_deg1.1112.04517726
X-RAY DIFFRACTIONr_angle_other_deg0.864321191
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.99151524
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.19823.54582
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.533152167
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.82215123
X-RAY DIFFRACTIONr_chiral_restr0.0570.22015
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02113983
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022538
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.4→3.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 115 -
Rwork0.254 1955 -
obs--100 %

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