3LX6 | pdb_00003lx6

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

• PDB DOI: https://doi.org/10.2210/pdb3LX6/pdb

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


• Deposited: 2010-02-24 Released: 2010-03-23 
• Deposition Author(s): Ramagopal, U.A., Toro, R., 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: 2.29 Å
• R-Value Free: 
  0.288 (Depositor), 0.291 (DCC) 
• R-Value Work: 
  0.243 (Depositor), 0.246 (DCC) 
• R-Value Observed: 
  0.245 (Depositor) 

Literature

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

Ramagopal, U.A., Toro, R., Burley, S.K., Almo, S.C.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 94.25 kDa 
• Atom Count: 5,835 
• Modeled Residue Count: 730 
• Deposited Residue Count: 820 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytosine-specific methyltransferase	A, B	410	Shigella flexneri 2a str. 2457T	Mutation(s): 0  Gene Names: 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, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.29 Å
• R-Value Free:  0.288 (Depositor), 0.291 (DCC) 
• R-Value Work:  0.243 (Depositor), 0.246 (DCC) 
• R-Value Observed: 0.245 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 122.957	α = 90
b = 83.807	β = 118.51
c = 113.236	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
HKL-2000	data reduction
SHELXE	model building
SHELXD	phasing
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-03-23 
Deposition Author(s): Ramagopal, U.A., Toro, R., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2010-03-23
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, 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: 2021-02-10
  Changes: Database references, Derived calculations, Structure summary
• Version 1.5: 2024-10-09
  Changes: Data collection, Database references, Structure summary