3ITB

Crystal structure of Penicillin-Binding Protein 6 (PBP6) from E. coli in complex with a substrate fragment

• PDB DOI: https://doi.org/10.2210/pdb3ITB/pdb

• Classification: HYDROLASE
• Organism(s): Escherichia coli, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-08-27 Released: 2009-10-20 
• Deposition Author(s): Chen, Y., Zhang, W., Shi, Q., Hesek, D., Lee, M., Mobashery, S., Shoichet, B.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.254 
• R-Value Work: 0.205 
• R-Value Observed: 0.207 

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Macromolecule Content

• Total Structure Weight: 154.08 kDa 
• Atom Count: 11,444 
• Modelled Residue Count: 1,394 
• Deposited Residue Count: 1,413 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-alanyl-D-alanine carboxypeptidase DacC	A, B, C, D	352	Escherichia coli	Mutation(s): 0  Gene Names: dacC, b0839, JW0823 EC: 3.4.16.4
UniProt
Find proteins for P08506 (Escherichia coli (strain K12)) Explore P08506  Go to UniProtKB:  P08506

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidoglycan substrate (AMV)A(FGA)K(DAL)(DAL)	E [auth L]	5	synthetic construct	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose	F [auth E]	2		N/A
Glycosylation Resources
GlyTouCan:  G05551OP GlyCosmos:  G05551OP

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AMV	M [auth F]	methyl 2-acetamido-3-O-[(1R)-1-carboxyethyl]-2-deoxy-beta-D-glucopyranoside C12 H21 N O8 UXEQYDNCHCKBIL-PKKPQKKZSA-N
SO4	G [auth A], H [auth B], I [auth B], J [auth B], K [auth C], L [auth D]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900003	F [auth E]	sucrose	Oligosaccharide / Nutrient

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.254 
• R-Value Work: 0.205 
• R-Value Observed: 0.207 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.534	α = 90
b = 185.351	β = 100.99
c = 82.329	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-10-20 
Deposition Author(s): Chen, Y., Zhang, W., Shi, Q., Hesek, D., Lee, M., Mobashery, S., Shoichet, B.K.

Revision History  

• Version 1.0: 2009-10-20
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2011-07-27
  Changes: Database references, Derived calculations, Non-polymer description
• Version 1.3: 2017-11-01
  Changes: Advisory, Refinement description
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
• Version 3.0: 2024-03-27
  Changes: Atomic model, Data collection, Database references, Derived calculations, Polymer sequence, Refinement description, Source and taxonomy, Structure summary
• Version 3.1: 2024-04-03
  Changes: Refinement description