3EEO | pdb_00003eeo

M. HhaI co-crystallized with synthetic dsDNA containing a propane diol in place of the deoxycytidine residue targeted for methylation.

• PDB DOI: https://doi.org/10.2210/pdb3EEO/pdb
• NAKB: 3EEO

• Classification: TRANSFERASE/DNA
• Organism(s): Haemophilus parahaemolyticus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-09-05 Released: 2010-03-02 
• Deposition Author(s): Porta, J.C., Christman, J.K., Borgstahl, G.E.O.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free: 
  0.275 (Depositor) 
• R-Value Work: 
  0.237 (Depositor), 0.240 (DCC) 
• R-Value Observed: 
  0.239 (Depositor) 

Literature

M. HhaI co-crystallized with synthetic dsDNA containing a propane diol in place of the deoxycytidine residue targeted for methylation.

Porta, J.C., Christman, J.K., Borgstahl, G.E.O.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 44.62 kDa 
• Atom Count: 3,226 
• Modeled Residue Count: 351 
• Deposited Residue Count: 351 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Modification methylase HhaI	C [auth A]	327	Haemophilus parahaemolyticus	Mutation(s): 0  Gene Names: hhaIM EC: 2.1.1.37
UniProt
Find proteins for P05102 (Haemophilus parahaemolyticus) Explore P05102  Go to UniProtKB:  P05102

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(P*DCP*DCP*DAP*DTP*DGP*DCP*DGP*DCP*DTP*DGP*DAP*DC)-3'	A [auth C]	12	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(P*DGP*DTP*DCP*DAP*DGP*(PDI)P*DGP*DCP*DAP*DTP*DGP*DG)-3'	B [auth D]	12	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAM	D [auth A]	S-ADENOSYLMETHIONINE C15 H22 N6 O5 S MEFKEPWMEQBLKI-FCKMPRQPSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free:  0.275 (Depositor) 
• R-Value Work:  0.237 (Depositor), 0.240 (DCC) 
• R-Value Observed: 0.239 (Depositor) 

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.479	α = 90
b = 95.479	β = 90
c = 318.353	γ = 120

Software Package:

Software Name	Purpose
CrystalClear	data collection
MOLREP	phasing
REFMAC	refinement
CrystalClear	data reduction
CrystalClear	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-03-02 
Deposition Author(s): Porta, J.C., Christman, J.K., Borgstahl, G.E.O.

Revision History  

• Version 1.0: 2010-03-02
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-02-21
  Changes: Data collection, Database references, Derived calculations