[English] 日本語
Yorodumi
- PDB-2dpm: DPNM DNA ADENINE METHYLTRANSFERASE FROM STREPTOCCOCUS PNEUMONIAE ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2dpm
TitleDPNM DNA ADENINE METHYLTRANSFERASE FROM STREPTOCCOCUS PNEUMONIAE COMPLEXED WITH S-ADENOSYLMETHIONINE
ComponentsPROTEIN (ADENINE-SPECIFIC METHYLTRANSFERASE DPNII 1)
KeywordsTRANSFERASE / DNA ADENINE METHYLTRANSFERASE / METHYLTRANSFERASE / METHYLASE / DNA METHYLTRANSFERASE GROUP ALPHA / S-ADENOSYLMETHIONINE / DNA N6-ADENINE METHYLATION / DPNII RESTRICTION-MODIFICATION SYSTEM / GATC METHYLATION / ROSSMANN FOLD
Function / homology
Function and homology information


site-specific DNA-methyltransferase (adenine-specific) / site-specific DNA-methyltransferase (adenine-specific) activity / S-adenosyl-L-methionine binding / DNA restriction-modification system / mismatch repair / methylation / sequence-specific DNA binding
Similarity search - Function
Adenine-specific Methyltransferase; domain 2 / Adenine-specific Methyltransferase, Domain 2 / Adenine modification methylase, M.EcoRV-type / D12 class N6 adenine-specific DNA methyltransferase / Adenine-specific methyltransferase, domain 2 / D12 class N6 adenine-specific DNA methyltransferase / N-6 Adenine-specific DNA methylases signature. / DNA methylase, N-6 adenine-specific, conserved site / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily ...Adenine-specific Methyltransferase; domain 2 / Adenine-specific Methyltransferase, Domain 2 / Adenine modification methylase, M.EcoRV-type / D12 class N6 adenine-specific DNA methyltransferase / Adenine-specific methyltransferase, domain 2 / D12 class N6 adenine-specific DNA methyltransferase / N-6 Adenine-specific DNA methylases signature. / DNA methylase, N-6 adenine-specific, conserved site / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / S-ADENOSYLMETHIONINE / Type II methyltransferase M1.DpnII
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsTran, P.H. / Korszun, Z.R. / Cerritelli, S. / Springhorn, S.S. / Lacks, S.A.
Citation
Journal: Structure / Year: 1998
Title: Crystal structure of the DpnM DNA adenine methyltransferase from the DpnII restriction system of streptococcus pneumoniae bound to S-adenosylmethionine.
Authors: Tran, P.H. / Korszun, Z.R. / Cerritelli, S. / Springhorn, S.S. / Lacks, S.A.
#1: Journal: J.Mol.Biol. / Year: 1989
Title: Crystallization of the DpnM Methylase from the DpnII Restriction System of Streptococcus Pneumoniae
Authors: Cerritelli, S. / White, S.W. / Lacks, S.A.
#2: Journal: J.Mol.Biol. / Year: 1987
Title: Proteins Encoded by the DpnII Restriction Gene Cassette. Two Methylases and an Endonuclease
Authors: de la Campa, A.G. / Kale, P. / Springhorn, S.S. / Lacks, S.A.
#3: Journal: Cell(Cambridge,Mass.) / Year: 1986
Title: Genetic Basis of the Complementary DpnI and DpnII Restriction Systems of S.pneumoniae: An Intercellular Cassette Mechanism
Authors: Lacks, S.A. / Mannarelli, B.M. / Springhorn, S.S. / Greenberg, B.
#4: Journal: Proc.Natl.Acad.Sci.USA / Year: 1985
Title: Nucleotide Sequence of the Dpn II DNA Methylase Gene of Streptococcus Pneumoniae and its Relationship to the dam Gene of Escherichia Coli
Authors: Mannarelli, B.M. / Balganesh, T.S. / Greenberg, B. / Springhorn, S.S. / Lacks, S.A.
History
DepositionSep 3, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Dec 23, 1998Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 12, 2014Group: Structure summary
Revision 1.4Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.5Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PROTEIN (ADENINE-SPECIFIC METHYLTRANSFERASE DPNII 1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5473
Polymers32,9481
Non-polymers5992
Water3,207178
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.600, 68.100, 85.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein PROTEIN (ADENINE-SPECIFIC METHYLTRANSFERASE DPNII 1) / M.DPNII 1


Mass: 32948.371 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: S-ADENOSYLMETHIONINE / Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: HB264 / Gene: DPNM / Plasmid: PLS211 / Gene (production host): DPNM / Production host: Escherichia coli (E. coli)
References: UniProt: P04043, site-specific DNA-methyltransferase (adenine-specific)
#2: Chemical ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Hg
#3: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


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


Mass: 18.015 Da / Num. of mol.: 178 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 48 % / Description: MAD DATA WERE TREATED AS MIRAS
Crystal growMethod: vapor diffusion, hanging drop / pH: 7
Details: FOR VAPOR DIFFUSION AT 4 C, HANGING DROPS CONTAINED 0.45 NM 0.9 NMOLS OF SAM, 100 MM HEPES BUFFER, PH 7.0, 250 MM NACL, 5% PEG 3350 IN 6 MICROLITERS. RESEVOIRS CONTAINED 1.0 ML OF 50.0 MM ...Details: FOR VAPOR DIFFUSION AT 4 C, HANGING DROPS CONTAINED 0.45 NM 0.9 NMOLS OF SAM, 100 MM HEPES BUFFER, PH 7.0, 250 MM NACL, 5% PEG 3350 IN 6 MICROLITERS. RESEVOIRS CONTAINED 1.0 ML OF 50.0 MM HEPES, 125 MM NACL, 2.5% PEG 3350., vapor diffusion - hanging drop
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.45 nmolprotein1drop
20.9 nmolAdoMet1drop
3100 mMHEPES1drop
4250 mM1dropNaCl
55 %(w/v)PEG33501drop
650 mMHEPES1reservoir
7125 mM1reservoirNaCl
82.5 %PEG33501reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.008, 1.011, 0.997, 0.968
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 15, 1996 / Details: MIRRORS
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.0081
21.0111
30.9971
40.9681
ReflectionResolution: 1.8→20 Å / Num. obs: 30274 / % possible obs: 99.9 % / Redundancy: 7 % / Rsym value: 0.05 / Net I/σ(I): 33.4
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 7 % / Mean I/σ(I) obs: 8.7 / Rsym value: 0.22 / % possible all: 100
Reflection
*PLUS
Num. measured all: 207177 / Rmerge(I) obs: 0.05
Reflection shell
*PLUS
% possible obs: 100 % / Num. unique obs: 1979 / Num. measured obs: 13527 / Rmerge(I) obs: 0.22

-
Processing

Software
NameVersionClassification
PHASESphasing
X-PLOR3.8refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 1.8→20 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.284 5730 10 %RANDOM
Rwork0.238 ---
obs0.238 57304 99.9 %-
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2088 0 29 178 2295
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_deg1.3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22.8
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.1
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
LS refinement shellResolution: 1.8→1.88 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.336 665 10.2 %
Rwork0.304 5840 -
obs--87 %
Xplor fileSerial no: 1 / Param file: PARHCSDX.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22.8
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.1
LS refinement shell
*PLUS
Rfactor Rfree: 0.336 / % reflection Rfree: 10.2 % / Rfactor Rwork: 0.304

+
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