3GRZ | pdb_00003grz

CRYSTAL STRUCTURE OF ribosomal protein L11 methylase FROM Lactobacillus delbrueckii subsp. bulgaricus

• PDB DOI: https://doi.org/10.2210/pdb3GRZ/pdb

• Classification: TRANSFERASE
• Organism(s): Lactobacillus delbrueckii subsp. bulgaricus ATCC BAA-365
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-03-26 Released: 2009-04-07 
• Deposition Author(s): Patskovsky, Y., Ramagopal, U.A., Toro, R., Morano, C., Freeman, J., Chang, S., 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: 2.00 Å
• R-Value Free: 
  0.225 (Depositor), 0.221 (DCC) 
• R-Value Work: 
  0.174 (Depositor) 
• R-Value Observed: 
  0.175 (Depositor) 

Literature

CRYSTAL STRUCTURE OF RIBOSOMAL PROTEIN 11 METHYLASE FROM Lactobacillus delbrueckii subsp. bulgaricus

Patskovsky, Y., Ramagopal, U.A., Toro, R., Morano, C., Freeman, J., Chang, S., Sauder, J.M., Burley, S.K., Almo, S.C.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 45.46 kDa 
• Atom Count: 3,312 
• Modeled Residue Count: 385 
• Deposited Residue Count: 410 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein L11 methyltransferase	A, B	205	Lactobacillus delbrueckii subsp. bulgaricus ATCC BAA-365	Mutation(s): 0  Gene Names: prmA, LBUL_0809 EC: 2.1.1
UniProt
Find proteins for Q04AV7 (Lactobacillus delbrueckii subsp. bulgaricus (strain ATCC BAA-365 / Lb-18)) Explore Q04AV7  Go to UniProtKB:  Q04AV7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A], D [auth A], E [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.225 (Depositor), 0.221 (DCC) 
• R-Value Work:  0.174 (Depositor) 
• R-Value Observed: 0.175 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 148.979	α = 90
b = 56.055	β = 90.92
c = 54.051	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-04-07 
Deposition Author(s): Patskovsky, Y., Ramagopal, U.A., Toro, R., Morano, C., Freeman, J., Chang, S., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2009-04-07
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2018-11-21
  Changes: Data collection, Structure summary
• Version 1.3: 2021-02-10
  Changes: Database references, Derived calculations, Structure summary
• Version 1.4: 2024-02-21
  Changes: Data collection, Database references