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- PDB-2dpm: DPNM DNA ADENINE METHYLTRANSFERASE FROM STREPTOCCOCUS PNEUMONIAE ... -

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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 / DNA restriction-modification system / nucleic acid 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 / Modification methylase DpnIIA
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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 / Mercury (element)


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


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


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

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Experimental details

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Experiment

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

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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

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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

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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

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