2UYH | pdb_00002uyh

HhaI DNA methyltransferase S87Q-Q237S mutant complex with 13mer GCGC- GMGC oligonucleotide and SAH

• PDB DOI: https://doi.org/10.2210/pdb2UYH/pdb
• NAKB: 2UYH

• Classification: TRANSFERASE
• Organism(s): Haemophilus haemolyticus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2007-04-06 Released: 2008-05-27 
• Deposition Author(s): Daujotyte, D., Grazulis, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.63 Å
• R-Value Free: 
  0.258 (Depositor), 0.258 (DCC) 
• R-Value Work: 
  0.199 (Depositor), 0.198 (DCC) 
• R-Value Observed: 
  0.199 (Depositor) 

Starting Model: experimental

Literature

HhaI DNA Methyltransferase S87Q-Q237S Mutant Complex with 13mer Gcgc-Gmgc Oligonucleotide and Sah

Daujotyte, D., Grazulis, S.

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: 45.46 kDa 
• Atom Count: 3,252 
• Modeled Residue Count: 352 
• Deposited Residue Count: 352 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MODIFICATION METHYLASE HHAI	A	327	Haemophilus haemolyticus	Mutation(s): 2  EC: 2.1.1.37
UniProt
Find proteins for P05102 (Haemophilus parahaemolyticus) Explore P05102  Go to UniProtKB:  P05102

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(*TP*GP*GP*AP*TP*G*5CMP*GP*CP*TP*GP *AP*C)-3'	B [auth C]	13	N/A

Entity ID: 3
Molecule	Chains	Length	Organism	Image
5'-D(*GP*TP*CP*AP*GP*CP*GP*CP*AP*TP *CP*C)-3'	C [auth D]	12	N/A

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAH	D [auth A]	S-ADENOSYL-L-HOMOCYSTEINE C14 H20 N6 O5 S ZJUKTBDSGOFHSH-WFMPWKQPSA-N
SO4	E [auth A], F [auth A], G [auth A], H [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.63 Å
• R-Value Free:  0.258 (Depositor), 0.258 (DCC) 
• R-Value Work:  0.199 (Depositor), 0.198 (DCC) 
• R-Value Observed: 0.199 (Depositor) 

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.382	α = 90
b = 95.382	β = 90
c = 312.972	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-05-27 
Deposition Author(s): Daujotyte, D., Grazulis, S.

Revision History  

• Version 1.0: 2008-05-27
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2019-07-24
  Changes: Data collection, Derived calculations
• Version 1.4: 2023-12-13
  Changes: Data collection, Database references, Other, Refinement description
• Version 1.5: 2025-12-10
  Changes: Data collection, Structure summary