[English] 日本語
Yorodumi
- PDB-1e3m: The crystal structure of E. coli MutS binding to DNA with a G:T m... -

+
Open data


ID or keywords:

Loading...

-
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 / regulation of DNA recombination / mismatch repair complex / mismatched DNA binding / DNA binding, bending / mismatch repair / ATP-dependent activity, acting on DNA / ADP binding / damaged DNA binding / cellular response to DNA damage stimulus ...adenine/cytosine mispair binding / regulation of DNA recombination / mismatch repair complex / mismatched DNA binding / DNA binding, bending / mismatch repair / ATP-dependent activity, acting on DNA / ADP binding / damaged DNA binding / cellular response to DNA damage stimulus / ATP binding / identical protein binding / cytosol
Similarity search - Function
Helix Hairpins - #80 / 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, N-terminal / MutS, connector domain superfamily / DNA mismatch repair protein MutS, connector domain ...Helix Hairpins - #80 / 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, N-terminal / MutS, connector domain superfamily / DNA mismatch repair protein MutS, connector domain / DNA mismatch repair protein MutS-like, N-terminal / MutS domain I / MutS domain II / MutS family domain IV / MutS domain III / DNA mismatch repair protein MutS, clamp / DNA-binding domain of DNA mismatch repair MUTS family / DNA mismatch repair proteins mutS family signature. / DNA mismatch repair protein MutS, C-terminal / DNA mismatch repair protein MutS, core domain superfamily / DNA mismatch repair protein MutS, core / MutS domain V / 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 / 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 (> 10) / DNA / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
γ
α
β
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

-
Components

-
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: NUCLEUSCell 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

-
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)

-
Non-polymers , 3 types, 481 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-MG / MAGNESIUM ION


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


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

-
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.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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 %

-
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

+
About Yorodumi

-
News

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

-
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

Result of Omokage search can be filtered by keywords and the database types

Related info.:Omokage search

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more