3G7U | pdb_00003g7u

Crystal structure of putative DNA modification methyltransferase encoded within prophage Cp-933R (E.coli)

• PDB DOI: https://doi.org/10.2210/pdb3G7U/pdb

• Classification: TRANSFERASE
• Organism(s): Escherichia coli O157:H7 str. EDL933
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-02-10 Released: 2009-02-24 
• Deposition Author(s): Patskovsky, Y., Ramagopal, U.A., Toro, R., Gilmore, M., Iizuka, M., 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: 
  0.219 (Depositor), 0.219 (DCC) 
• R-Value Work: 
  0.183 (Depositor), 0.183 (DCC) 
• R-Value Observed: 
  0.184 (Depositor) 

Literature

Crystal Structure of DNA Modification Methyltransferase Encoded within Prophage Cp-933R (E.coli)

Patskovsky, Y., Ramagopal, U.A., Toro, R., Gilmore, M., Iizuka, M., 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: 42.52 kDa 
• Atom Count: 3,166 
• Modeled Residue Count: 348 
• Deposited Residue Count: 376 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytosine-specific methyltransferase	A	376	Escherichia coli O157:H7 str. EDL933	Mutation(s): 0  Gene Names: ECs1953, Z2389 EC: 2.1.1.37
UniProt
Find proteins for Q8X8S5 (Escherichia coli O157:H7) Explore Q8X8S5  Go to UniProtKB:  Q8X8S5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A], D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	B [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free:  0.219 (Depositor), 0.219 (DCC) 
• R-Value Work:  0.183 (Depositor), 0.183 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.436	α = 90
b = 79.436	β = 90
c = 126.539	γ = 120

Software Package:

Software Name	Purpose
MAR345	data collection
SHELXD	phasing
REFMAC	refinement
DENZO	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-02-24 
Deposition Author(s): Patskovsky, Y., Ramagopal, U.A., Toro, R., Gilmore, M., Iizuka, M., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2009-02-24
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2018-11-21
  Changes: Data collection, Structure summary
• Version 1.4: 2021-02-10
  Changes: Database references, Derived calculations, Structure summary
• Version 1.5: 2024-02-21
  Changes: Data collection, Database references