Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 87163.48 
• Atom Count: 5638 
• Residue Count: 768 
• Unique protein chains: 1

3VMA

Crystal Structure of the Full-Length Transglycosylase PBP1b from Escherichia coli

• DOI: 10.2210/pdb3VMA/pdb
• Entry 3VMA supersedes 3FWM

• Classification: TRANSFERASE HYDROLASE/ANTIBIOTIC
• Organism(s): Escherichia coli (strain K12)
• Expression System: Escherichia coli


• Deposited: 2011-12-09 Released: 2012-03-14 
• Deposition Author(s): Huang, C.Y., Sung, M.T., Lai, Y.T., Chou, L.Y., Shih, H.W., Cheng, W.C., Wong, C.H., Ma, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.161 Å
• R-Value Free: 0.250 
• R-Value Work: 0.212 

Literature

Crystal structure of the membrane-bound bifunctional transglycosylase PBP1b from Escherichia coli.

Sung, M.T., Lai, Y.T., Huang, C.Y., Chou, L.Y., Shih, H.W., Cheng, W.C., Wong, C.H., Ma, C.

(2009) Proc.Natl.Acad.Sci.USA 106: 8824-8829

• PubMed: 19458048 
• DOI: 10.1073/pnas.0904030106
• Primary Citation of Related Structures:  
  3FWM, 3FWL


• PubMed Abstract: 
  

Drug-resistant bacteria have caused serious medical problems in recent years, and the need for new antibacterial agents is undisputed. Transglycosylase, a multidomain membrane protein essential for cell wall synthesis, is an excellent target for the development of new antibiotics. Here, we determined the X-ray crystal structure of the bifunctional transglycosylase penicillin-binding protein 1b (PBP1b) from Escherichia coli in complex with its inhibitor moenomycin to 2.16-A resolution. In addition to the transglycosylase and transpeptidase domains, our structure provides a complete visualization of this important antibacterial target, and reveals a domain for protein-protein interaction and a transmembrane helix domain essential for substrate binding, enzymatic activity, and membrane orientation.

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Organizational Affiliation: 

Genomics Research Center, Academia Sinica, 128 Academia Road, Section 2, Taipei 115, Taiwan.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Penicillin-binding protein 1B	A	768	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: mrcB (pbpF, ponB) EC: 2.4.1.129, 3.4.16.4
Membrane protein mpstruct	Group:  MONOTOPIC MEMBRANE PROTEINS		Sub Group:  Glycosyltransferases	Protein:  Peptidoglycan Glycosyltransferase penicillin-binding protein 1b (PBP1b)
Find proteins for P02919 (Escherichia coli (strain K12)) Go to UniProtKB:  P02919

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
M0E	A	MOENOMYCIN MOENOMYCIN C69 H106 N5 O34 P NXPRJQIAIORCGO-ZLPAOQQDSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.161 Å
• R-Value Free: 0.250 
• R-Value Work: 0.212 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length (Å)	Angle (°)
a = 62.900	α = 90.00
b = 289.530	β = 90.00
c = 62.780	γ = 90.00

Software Package:

Software Name	Purpose
SOLVE	phasing
HKL-2000	data reduction
HKL-2000	data collection
HKL-2000	data scaling
PHENIX	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-12-09 
• Released Date: 2012-03-14 
• Deposition Author(s): Huang, C.Y., Sung, M.T., Lai, Y.T., Chou, L.Y., Shih, H.W., Cheng, W.C., Wong, C.H., Ma, C.
• This entry supersedes: 3FWM

Revision History 

• Version 1.0: 2012-03-14
  Type: Initial release