[English] 日本語
Yorodumi
- PDB-1nne: Crystal Structure of the MutS-ADPBeF3-DNA complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1nne
TitleCrystal Structure of the MutS-ADPBeF3-DNA complex
Components
  • 5'-D(*GP*CP*GP*AP*CP*GP*CP*TP*AP*GP*CP*GP*TP*GP*CP*GP*GP*CP*TP*CP*GP*TP*C)-3'
  • 5'-D(P*GP*GP*AP*CP*GP*AP*GP*CP*CP*GP*CP*CP*GP*CP*TP*AP*GP*CP*GP*TP*CP*G)-3'
  • DNA Mismatch Repair protein MutS
KeywordsDNA BINDING PROTEIN/DNA / DNA / DNA BINDING PROTEIN-DNA COMPLEX
Function / homology
Function and homology information


mismatched DNA binding / ATP-dependent DNA damage sensor activity / mismatch repair / damaged DNA binding / ATP binding
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 / BERYLLIUM TRIFLUORIDE ION / DNA / DNA (> 10) / DNA mismatch repair protein MutS
Similarity search - Component
Biological speciesThermus aquaticus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.11 Å
AuthorsAlani, E. / Lee, J.Y. / Schofield, M.J. / Kijas, A.W. / Hsieh, P. / Yang, W.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Crystal structure and biochemical analysis of the MutS-ADP-Beryllium Fluoride complex suggests a conserved mechanism for ATP interactions in mismatch repair
Authors: Alani, E. / Lee, J.Y. / Schofield, M.J. / Kijas, A.W. / Hsieh, P. / Yang, W.
History
DepositionJan 13, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
C: 5'-D(*GP*CP*GP*AP*CP*GP*CP*TP*AP*GP*CP*GP*TP*GP*CP*GP*GP*CP*TP*CP*GP*TP*C)-3'
D: 5'-D(P*GP*GP*AP*CP*GP*AP*GP*CP*CP*GP*CP*CP*GP*CP*TP*AP*GP*CP*GP*TP*CP*G)-3'
A: DNA Mismatch Repair protein MutS
B: DNA Mismatch Repair protein MutS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)186,64711
Polymers185,4074
Non-polymers1,2417
Water1,78399
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)103.442, 113.224, 160.284
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
DNA chain , 2 types, 2 molecules CD

#1: DNA chain 5'-D(*GP*CP*GP*AP*CP*GP*CP*TP*AP*GP*CP*GP*TP*GP*CP*GP*GP*CP*TP*CP*GP*TP*C)-3'


Mass: 7074.534 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(P*GP*GP*AP*CP*GP*AP*GP*CP*CP*GP*CP*CP*GP*CP*TP*AP*GP*CP*GP*TP*CP*G)-3'


Mass: 6779.355 Da / Num. of mol.: 1 / Source method: obtained synthetically

-
Protein , 1 types, 2 molecules AB

#3: Protein DNA Mismatch Repair protein MutS /


Mass: 85776.477 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus aquaticus (bacteria) / References: UniProt: Q56215

-
Non-polymers , 5 types, 106 molecules

#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: BeF3
#6: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 99 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.56 Å3/Da / Density % sol: 51.6 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 6.2
Details: 200 mM Ammonium sulfate, 1 mM DTT, 18% PEG4000, 100 mM cacodylate, VAPOR DIFFUSION, HANGING DROP, pH 6.2
Components of the solutions
IDNameCrystal-IDSol-ID
1200 mM Ammonium sulfate11
21 mM DTT11
318% PEG400011
4100 mM cacodylate11
5Ammonium sulfate12
6DTT12
7PEG400012
8cacodylateCacodylic acid12
Crystal grow
*PLUS
Temperature: 20 ℃ / Details: Obmolova, G., (2000) Nature, 407, 703.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.5-15 mg/mlprotein1drop
2100 mMcacodylate1reservoir
3200 mMammonium sulfate1reservoir
41 mMdithiothreitol1reservoir
518 %PEG40001reservoir
61
71
81

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 3.1→20 Å / Num. obs: 31754 / % possible obs: 92.4 % / Observed criterion σ(I): 1 / Rsym value: 0.114
Reflection shellResolution: 3.11→3.15 Å / Rmerge(I) obs: 0.493 / Mean I/σ(I) obs: 2.1 / % possible all: 86.3
Reflection
*PLUS
Lowest resolution: 20 Å / Rmerge(I) obs: 0.114
Reflection shell
*PLUS
Highest resolution: 3.1 Å / % possible obs: 86.3 %

-
Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.11→19.94 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 193504.68 / Data cutoff high rms absF: 193504.68 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.259 1495 5 %RANDOM
Rwork0.209 ---
obs0.209 30076 87.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 10 Å2 / ksol: 0.228094 e/Å3
Displacement parametersBiso mean: 41 Å2
Baniso -1Baniso -2Baniso -3
1--9.84 Å20 Å20 Å2
2--5.9 Å20 Å2
3---3.94 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.63 Å0.52 Å
Refinement stepCycle: LAST / Resolution: 3.11→19.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11992 922 76 99 13089
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.15
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.791.5
X-RAY DIFFRACTIONc_mcangle_it4.782
X-RAY DIFFRACTIONc_scbond_it4.252
X-RAY DIFFRACTIONc_scangle_it7.082.5
LS refinement shellResolution: 3.1→3.29 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.382 197 4.8 %
Rwork0.313 3905 -
obs--71.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3ION.PARAMWATER.TOP
X-RAY DIFFRACTION4WATER_REP.PARAMION.TOP
X-RAY DIFFRACTION5ABF.PARAMABF.TOP
Refinement
*PLUS
Highest resolution: 3.1 Å / Lowest resolution: 20 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.596
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.15

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
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

-
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