[English] 日本語
Yorodumi
- PDB-6mht: TERNARY STRUCTURE OF HHAI METHYLTRANSFERASE WITH ADOHCY AND DNA C... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6mht
TitleTERNARY STRUCTURE OF HHAI METHYLTRANSFERASE WITH ADOHCY AND DNA CONTAINING 4'-THIO-2'DEOXYCYTIDINE AT THE TARGET
Components
  • CYTOSINE-SPECIFIC METHYLTRANSFERASE HHAI
  • DNA (5'-D(P*CP*CP*AP*TP*GP*(5CM)P*GP*CP*TP*GP*AP*C)-3')
  • DNA (5'-D(P*GP*TP*CP*AP*GP*(4SC)P*GP*CP*AP*TP*GP*G)-3')
KeywordsTRANSFERASE/DNA / TRANSFERASE / METHYLTRANSFERASE / RESTRICTION SYSTEM / COMPLEX (METHYLTRANSFERASE-DNA) / TRANSFERASE-DNA complex
Function / homology
Function and homology information


DNA (cytosine-5-)-methyltransferase / DNA (cytosine-5-)-methyltransferase activity / DNA restriction-modification system / methylation / DNA binding
Similarity search - Function
: / DNA Methylase, subunit A, domain 2 / DNA Methylase; Chain A, domain 2 / DNA methylase, C-5 cytosine-specific, conserved site / C-5 cytosine-specific DNA methylases C-terminal signature. / DNA methylase, C-5 cytosine-specific, active site / C-5 cytosine-specific DNA methylases active site. / C-5 cytosine-specific DNA methylase (Dnmt) domain profile. / C-5 cytosine methyltransferase / C-5 cytosine-specific DNA methylase ...: / DNA Methylase, subunit A, domain 2 / DNA Methylase; Chain A, domain 2 / DNA methylase, C-5 cytosine-specific, conserved site / C-5 cytosine-specific DNA methylases C-terminal signature. / DNA methylase, C-5 cytosine-specific, active site / C-5 cytosine-specific DNA methylases active site. / C-5 cytosine-specific DNA methylase (Dnmt) domain profile. / C-5 cytosine methyltransferase / C-5 cytosine-specific DNA methylase / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYLMETHIONINE / DNA / DNA (> 10) / Type II methyltransferase M.HhaI
Similarity search - Component
Biological speciesHaemophilus haemolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.05 Å
AuthorsCheng, X.
CitationJournal: Nucleic Acids Res. / Year: 1997
Title: DNA containing 4'-thio-2'-deoxycytidine inhibits methylation by HhaI methyltransferase.
Authors: Kumar, S. / Horton, J.R. / Jones, G.D. / Walker, R.T. / Roberts, R.J. / Cheng, X.
History
DepositionAug 5, 1998Deposition site: NDB / Processing site: NDB
Revision 1.0Aug 12, 1998Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Apr 13, 2022Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / entity / struct_conn / struct_site
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Aug 2, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
C: DNA (5'-D(P*CP*CP*AP*TP*GP*(5CM)P*GP*CP*TP*GP*AP*C)-3')
D: DNA (5'-D(P*GP*TP*CP*AP*GP*(4SC)P*GP*CP*AP*TP*GP*G)-3')
A: CYTOSINE-SPECIFIC METHYLTRANSFERASE HHAI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8124
Polymers44,4133
Non-polymers3981
Water2,666148
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)99.860, 99.860, 325.200
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Cell settinghexagonal
Space group name H-MH32

-
Components

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


Mass: 3637.395 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus haemolyticus (bacteria) / Production host: Escherichia coli (E. coli)
#2: DNA chain DNA (5'-D(P*GP*TP*CP*AP*GP*(4SC)P*GP*CP*AP*TP*GP*G)-3')


Mass: 3733.508 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
#3: Protein CYTOSINE-SPECIFIC METHYLTRANSFERASE HHAI / E.C.2.1.1.73 / MODIFICATION METHYLASE HHAI / M.HHAI


Mass: 37042.207 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus haemolyticus (bacteria) / References: UniProt: P05102, EC: 2.1.1.73
#4: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.52 Å3/Da / Density % sol: 65.02 %
Crystal growTemperature: 293 K / pH: 5.6
Details: 1.4-1.8 M AMMONIUM SULFATE 50 MM CITRATE PH 5.6, temperature 293.0K
Components of the solutions
IDNameCrystal-IDSol-ID
1(NH4)2SO411
2citrate11
3(NH4)2SO412
Crystal grow
*PLUS
Temperature: 16 ℃ / Method: unknown / Details: O'Gara, M., (1996) J. Mol. Biol., 261, 634.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1
21.4-1.8 Mammonium sulfate1
350 mMcitrate11
41.4-1.8 Mammonium sulfate12
550 mMcitrate12

-
Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.15
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.15 Å / Relative weight: 1
ReflectionResolution: 2.05→20 Å / Num. obs: 32880 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.33 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 12.1

-
Processing

Software
NameVersionClassification
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: OTHER
Starting model: PDB ENTRY 5MHT

5mht


Resolution: 2.05→5 Å / Rfactor Rfree error: 0.004 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.231 2998 8.1 %Random
Rwork0.186 ---
obs-30012 81.6 %-
Refinement stepCycle: LAST / Resolution: 2.05→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2607 492 29 148 3276
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.8
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.3
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.6
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.186
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.3
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.6

+
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