3ME5 | pdb_00003me5

Crystal structure of putative dna cytosine methylase from shigella flexneri 2a str. 2457T

• PDB DOI: https://doi.org/10.2210/pdb3ME5/pdb

• Classification: TRANSFERASE
• Organism(s): Shigella flexneri 2a str. 2457T
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-03-31 Released: 2010-04-21 
• Deposition Author(s): Ramagopal, U.A., Malashkevich, V.N., Toro, R., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 
  0.261 (Depositor), 0.299 (DCC) 
• R-Value Work: 
  0.220 (Depositor) 
• R-Value Observed: 
  0.222 (Depositor) 

Literature

Crystal structure of putative dna cytosine methylase from shigella flexneri 2a str. 2457T

Ramagopal, U.A., Malashkevich, V.N., Toro, R., Sauder, J.M., Burley, S.K., Almo, S.C.

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: 55.27 kDa 
• Atom Count: 3,628 
• Modeled Residue Count: 414 
• Deposited Residue Count: 482 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytosine-specific methyltransferase	A	482	Shigella flexneri 2a str. 2457T	Mutation(s): 0  Gene Names: AAP17376.1, dcm, S2100, SF2005, SF2457T_1495 EC: 2.1.1.37

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free:  0.261 (Depositor), 0.299 (DCC) 
• R-Value Work:  0.220 (Depositor) 
• R-Value Observed: 0.222 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 149.629	α = 90
b = 51.593	β = 90
c = 63.026	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-04-21 
Deposition Author(s): Ramagopal, U.A., Malashkevich, V.N., Toro, R., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2010-04-21
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Refinement description, Version format compliance
• Version 1.2: 2012-05-23
  Changes: Database references, Source and taxonomy
• Version 1.3: 2017-11-08
  Changes: Refinement description
• Version 1.4: 2018-11-21
  Changes: Data collection, Structure summary
• Version 1.5: 2021-02-10
  Changes: Database references, Derived calculations, Structure summary
• Version 1.6: 2024-11-06
  Changes: Data collection, Database references, Structure summary