2C7R

HhaI DNA methyltransferase complex with oligonucleotide containing 2- aminopurine as a target base (GPGC:GMGC) and SAH

Structural Biology Knowledgebase: 2C7R SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.217
  • R-Value Work: 0.199

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2C7R

Classification: TRANSFERASE / DNA

Total Structure Weight: 45880.67


Macromolecule Entities
Molecule Chains Length Organism Details
MODIFICATION METHYLASE HHAI A 327 Haemophilus haemolyticus EC#: 2.1.1.37 IUBMB
Mutation: T250G
Gene Name(s): hhaIM
Macromolecule Entities
Molecule Chains Length Organism Details
5'-D(*G*GP*AP*TP*GP*(5CM)*GP*CP*TP*GP*AP*C)-3' C 12 Synthetic construct
5'-D(*G*TP*CP*AP*GP*(2PR)*GP*CP*AP*TP*CP*C)-3' D 12 Synthetic construct

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
SAH
Query on SAH

A S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

A SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

A GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 2 Unique
ID Chains Type Formula 2D Diagram Parent
5CM
Query on 5CM
C DNA LINKING C10 H16 N3 O7 P DC
2PR
Query on 2PR
D DNA LINKING C10 H14 N5 O6 P DG

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.217
  • R-Value Work: 0.199
  • Space Group: H 3 2

Unit Cell:

Length (Å) Angle (°)
a = 95.62 α = 90.00
b = 95.62 β = 90.00
c = 315.76 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2005-11-27
  • Released Date: 2005-12-14
  • Deposition author(s): Daujotyte, D., Grazulis, S.

Revision History

  • 2014-01-29
    Type: Biological assembly | Details: REMARK 300,REMARK 350
  • 2014-01-29
    Type: Linkage | Details: LINK
  • 2014-01-29
    Type: Polymer description | Details: COMPND,SEQRES
  • 2014-01-29
    Type: Refinement description | Details: REMARK 3
  • 2014-01-29
    Type: Other | Details: REMARK 375,MODRES,HEADER,REMARK 525
  • 2014-01-29
    Type: Non-polymer description | Details: HETSYN,FORMUL,HETNAM,HET
  • 2014-01-29
    Type: Geometry validation | Details: REMARK 500
  • 2014-01-29
    Type: Version format compliance | Details: REMARK 4
  • 2014-01-29
    Type: Function and keywords | Details: KEYWDS
  • 2014-01-29
    Type: Source and taxonomy | Details: SOURCE
  • 2014-01-29
    Type: Atom nomenclature | Details: HETATM