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- PDB-1e3m: The crystal structure of E. coli MutS binding to DNA with a G:T m... -

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Basic information

Entry
Database: PDB / ID: 1e3m
TitleThe crystal structure of E. coli MutS binding to DNA with a G:T mismatch
Components
  • 5'-D(*AP*GP*CP*TP*GP*CP*CP*AP*GP*GP*CP*AP*CP*CP*AP* GP*TP*GP*TP*CP*AP*GP*CP*GP*TP*CP*CP*TP*AP*T)-3'
  • 5'-D(*AP*TP*AP*GP*GP*AP*CP*GP*CP*TP*GP*AP*CP*AP*CP* TP*GP*GP*TP*GP*CP*TP*TP*GP*GP*CP*AP*GP*CP*T)-3'
  • DNA MISMATCH REPAIR PROTEIN MUTS
KeywordsDNA BINDING / MISMATCH RECOGNITION
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
Helix Hairpins - #80 / MutS, DNA mismatch repair protein; Chain A, domain 3 / MutS, DNA mismatch repair protein; Chain A, domain 3 - #10 / MutS, connector domain / DNA repair protein MutS, domain I / 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 ...Helix Hairpins - #80 / MutS, DNA mismatch repair protein; Chain A, domain 3 / MutS, DNA mismatch repair protein; Chain A, domain 3 - #10 / MutS, connector domain / DNA repair protein MutS, domain I / 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 / Helix Hairpins / Helix non-globular / Special / Nucleotidyltransferase; domain 5 / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsLamers, M.H. / Perrakis, A. / Enzlin, J.H. / Winterwerp, H.H.K. / De Wind, N. / Sixma, T.K.
CitationJournal: Nature / Year: 2000
Title: The Crystal Structure of DNA Mismatch Repair Protein Muts Binding to a G X T Mismatch
Authors: Lamers, M.H. / Perrakis, A. / Enzlin, J.H. / Winterwerp, H.H.K. / De Wind, N. / Sixma, T.K.
History
DepositionJun 19, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 1, 2000Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2014Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Refinement description / Source and taxonomy / Structure summary / Version format compliance
Revision 1.2Jul 5, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_entry_details.has_protein_modification / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: 5'-D(*AP*GP*CP*TP*GP*CP*CP*AP*GP*GP*CP*AP*CP*CP*AP* GP*TP*GP*TP*CP*AP*GP*CP*GP*TP*CP*CP*TP*AP*T)-3'
F: 5'-D(*AP*TP*AP*GP*GP*AP*CP*GP*CP*TP*GP*AP*CP*AP*CP* TP*GP*GP*TP*GP*CP*TP*TP*GP*GP*CP*AP*GP*CP*T)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)200,4007
Polymers199,9254
Non-polymers4763
Water8,611478
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11350 Å2
ΔGint-95.7 kcal/mol
Surface area70310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.960, 92.370, 261.330
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


Mass: 90729.859 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-800
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Cellular location: NUCLEUS / Gene: MUTS / Cellular location (production host): CYTOPLASM / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): PLYSS / References: UniProt: P23909

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DNA chain , 2 types, 2 molecules EF

#2: DNA chain 5'-D(*AP*GP*CP*TP*GP*CP*CP*AP*GP*GP*CP*AP*CP*CP*AP* GP*TP*GP*TP*CP*AP*GP*CP*GP*TP*CP*CP*TP*AP*T)-3'


Mass: 9184.905 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA OLIGONUCLEOTIDES, ANNEALED / Source: (synth.) ESCHERICHIA COLI (E. coli)
#3: DNA chain 5'-D(*AP*TP*AP*GP*GP*AP*CP*GP*CP*TP*GP*AP*CP*AP*CP* TP*GP*GP*TP*GP*CP*TP*TP*GP*GP*CP*AP*GP*CP*T)-3'


Mass: 9279.964 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA OLIGONUCLEOTIDES, ANNEALED / Source: (synth.) ESCHERICHIA COLI (E. coli)

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Non-polymers , 3 types, 481 molecules

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


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


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 478 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsFUNCTION: THIS PROTEIN IS INVOLVED IN THE REPAIR OF MISMATCHES IN DNA. IT IS POSSIBLE THAT IT CARRY ...FUNCTION: THIS PROTEIN IS INVOLVED IN THE REPAIR OF MISMATCHES IN DNA. IT IS POSSIBLE THAT IT CARRY OUT THE MISMATCH RECOGNITION STEP. THIS PROTEIN HAS A WEAK ATPASE ACTIVITY. SIMILARITY: BELONGS TO THE DNA MISMATCH REPAIR MUTS FAMILY.
Has protein modificationY

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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: 2.7 Å3/Da / Density % sol: 55 % / Description: MAD DATA WERE COLLECTED IN ESRF BM14
Crystal growpH: 7
Details: 12-14 % PEG 6000, 150-300 MM NACL, 100 MM HEPES PH 7-8, 10 MM MGCL2, 100-150 MICROM ADP
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop / Details: used microseeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
114 mg/mlprotein1drop
225 mMHEPES1drop
3250 mM1dropNaCl
410-20 mMbeta-mercaptoethanol1drop
512-14 %PEG60001reservoir
6150-300 mM1reservoirNaCl
7100 mMHEPES1reservoir
810 mM1reservoirMgCl2
90.100-0.150 mMADP1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 15, 2000
RadiationMonochromator: SI111 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. obs: 109670 / % possible obs: 98.7 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 15.9
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.469 / Mean I/σ(I) obs: 2.2 / % possible all: 95.1
Reflection shell
*PLUS
% possible obs: 95.1 %

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Processing

Software
NameVersionClassification
REFMAC5refinement
HKL-2000data reduction
HKL-2000data scaling
SnBphasing
MLPHAREphasing
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.2→20 Å / SU B: 7.181 / SU ML: 0.183 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.253 / ESU R Free: 0.209 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.266 2197 2 %RANDOM
Rwork0.228 ---
obs0.229 107405 98.7 %-
Displacement parametersBiso mean: 46.62 Å2
Baniso -1Baniso -2Baniso -3
1--1.06 Å20 Å20 Å2
2--3.76 Å20 Å2
3----2.7 Å2
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12171 714 29 478 13392
Software
*PLUS
Name: REFMAC / Version: 5 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.22891 / Rfactor Rfree: 0.26613 / Rfactor Rwork: 0.22814
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 46.622 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONp_bond_d0.012
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.173
X-RAY DIFFRACTIONp_mcbond_it1.5
X-RAY DIFFRACTIONp_scbond_it3
X-RAY DIFFRACTIONp_mcangle_it2
X-RAY DIFFRACTIONp_scangle_it4.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.367 / Rfactor obs: 0.324

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