[English] 日本語
Yorodumi
- PDB-1b62: MUTL COMPLEXED WITH ADP -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 1b62
TitleMUTL COMPLEXED WITH ADP
ComponentsPROTEIN (MUTL)
KeywordsDNA MISMATCH REPAIR / ATPASE
Function / homologyHistidine kinase-, DNA gyrase B-, and HSP90-like ATPase / MutL, C-terminal, dimerisation / DNA mismatch repair proteins mutL / hexB / PMS1 signature. / MutL C terminal dimerisation domain / DNA mismatch repair protein, C-terminal domain / DNA mismatch repair protein MutL/Mlh/Pms / MutL, C-terminal domain superfamily / Histidine kinase/HSP90-like ATPase superfamily / DNA mismatch repair protein, MutL / Ribosomal protein S5 domain 2-type fold ...Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / MutL, C-terminal, dimerisation / DNA mismatch repair proteins mutL / hexB / PMS1 signature. / MutL C terminal dimerisation domain / DNA mismatch repair protein, C-terminal domain / DNA mismatch repair protein MutL/Mlh/Pms / MutL, C-terminal domain superfamily / Histidine kinase/HSP90-like ATPase superfamily / DNA mismatch repair protein, MutL / Ribosomal protein S5 domain 2-type fold / DNA mismatch repair, conserved site / Ribosomal protein S5 domain 2-type fold, subgroup / DNA mismatch repair protein, S5 domain 2-like / Histidine kinase/HSP90-like ATPase / DNA mismatch repair protein family, N-terminal / regulation of DNA recombination / mismatch repair complex / mismatched DNA binding / mismatch repair / ATPase activity / DNA binding / ATP binding / identical protein binding / DNA mismatch repair protein MutL
Function and homology information
Specimen sourceEscherichia coli K12 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / 2.1 Å resolution
AuthorsWei, Y.
CitationJournal: Cell(Cambridge,Mass.) / Year: 1999
Title: Transformation of MutL by ATP binding and hydrolysis: a switch in DNA mismatch repair.
Authors: Ban, C. / Junop, M. / Yang, W.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jan 11, 1999 / Release: Apr 28, 1999
RevisionDateData content typeGroupProviderType
1.0Apr 28, 1999Structure modelrepositoryInitial release
1.1Apr 26, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelDerived calculations / Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PROTEIN (MUTL)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2983
Polyers39,8461
Non-polymers4522
Water4,270237
1
A: PROTEIN (MUTL)
hetero molecules

A: PROTEIN (MUTL)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,5956
Polyers79,6922
Non-polymers9034
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area (Å2)6420
ΔGint (kcal/M)-62
Surface area (Å2)29160
MethodPISA,PQS
Unit cell
γ
α
β
Length a, b, c (Å)62.330, 72.630, 190.120
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI 2 2 2

-
Components

#1: Protein/peptide PROTEIN (MUTL)


Mass: 39846.203 Da / Num. of mol.: 1 / Fragment: ATPASE FRAGMENT / Source: (gene. exp.) Escherichia coli K12 (bacteria) / Genus: Escherichia / Species: Escherichia coli / Strain: K-12 / Description: HIS-TAGGED / Gene: MUTL / Plasmid name: PTX418 / Genus (production host): Escherichia / Gene (production host): MUTL / Production host: Escherichia coli (E. coli) / Strain (production host): HMS174 (LAMBDA DE3) / References: UniProt: P23367
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Formula: Mg / Magnesium
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Formula: C10H15N5O10P2 / Adenosine diphosphate / Comment: ADP (energy-carrying molecule) *YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 237 / Formula: H2O / Water

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.7 / Density percent sol: 55 %
Crystal growpH: 8.5 / Details: pH 8.5
Crystal grow
*PLUS
Temp: 20 ℃ / Method: vapor diffusion, hanging drop
components of the solutions
*PLUS
IDConcCommon nameCrystal IDSol IDChemical formula
1100 mMTris1reservoir
2400 mM1reservoirLi2SO4
32 mMdithiothreitol1reservoir
428 %PEG5000 MME1reservoir

-
Data collection

DiffractionMean temperature: 98 kelvins
SourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Details: MIRRORS / Detector: IMAGE PLATE / Collection date: Jul 1, 1998
RadiationMonochromator: NI FILTER / Diffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionB iso Wilson estimate: 22.7 Å2 / D resolution high: 2.1 Å / D resolution low: 2 Å / Number obs: 24672 / Rsym value: 0.079 / NetI over sigmaI: 14.4 / Redundancy: 11.2 % / Percent possible obs: 97.6
Reflection shellHighest resolution: 2.1 Å / Lowest resolution: 2.14 Å / MeanI over sigI obs: 2 / Rsym value: 0.357 / Redundancy: 2.8 % / Percent possible all: 93.6
Reflection
*PLUS
Rmerge I obs: 0.079
Reflection shell
*PLUS
Percent possible obs: 93.6 / Rmerge I obs: 0.357

+
Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefineMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: BNL-26192

R Free selection details: RANDOM / Data cutoff high rms absF: 365343.51 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / Sigma F: 0
Solvent computationSolvent model details: FLAT MODEL / Solvent model param bsol: 36.6 / Solvent model param ksol: 0.333
Displacement parametersB iso mean: 44.7 Å2 / Aniso B11: -3 Å2 / Aniso B12: 0 Å2 / Aniso B13: 0 Å2 / Aniso B22: 0.22 Å2 / Aniso B23: 0 Å2 / Aniso B33: 2.77 Å2
Least-squares processR factor R free: 0.253 / R factor R free error: 0.007 / R factor R work: 0.231 / Highest resolution: 2.1 Å / Lowest resolution: 2 Å / Number reflection R free: 1192 / Number reflection obs: 24663 / Percent reflection R free: 4.8 / Percent reflection obs: 96.1
Refine analyzeLuzzati coordinate error free: 0.31 Å / Luzzati coordinate error obs: 0.28 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a free: 0.27 Å / Luzzati sigma a obs: 0.22 Å
Refine hist #LASTHighest resolution: 2.1 Å / Lowest resolution: 2 Å
Number of atoms included #LASTProtein: 2603 / Nucleic acid: 0 / Ligand: 28 / Solvent: 237 / Total: 2868
Refine LS restraints
Refine IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
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_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.76
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.821.5
X-RAY DIFFRACTIONc_mcangle_it1.432.00
X-RAY DIFFRACTIONc_scbond_it1.232.00
X-RAY DIFFRACTIONc_scangle_it1.972.50
Refine LS shellHighest resolution: 2.1 Å / R factor R free: 0.298 / R factor R free error: 0.022 / R factor R work: 0.286 / Lowest resolution: 2.23 Å / Number reflection R free: 184 / Number reflection R work: 3710 / Total number of bins used: 6 / Percent reflection R free: 4.7 / Percent reflection obs: 91.9
Xplor file
Refine IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4ADP.PARAMADP.TOP
Software
*PLUS
Name: CNS / Version: 0.3 / Classification: refinement
Least-squares process
*PLUS
R factor obs: 0.231
Refine LS restraints
*PLUS
Refine IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.76

+
About Yorodumi

-
News

-
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. (see PDBe EMDB page)
  • 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 at EBI / 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. See below links for details.
  • 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

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

Read more

-
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.

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