6NHU | pdb_00006nhu

Crystal Structure of the Beta Lactamase Class D YbxI from Agrobacterium fabrum

• PDB DOI: https://doi.org/10.2210/pdb6NHU/pdb

• Classification: HYDROLASE
• Organism(s): Agrobacterium fabrum str. C58
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2018-12-23 Released: 2019-01-16 
• Deposition Author(s): Kim, Y., Welk, L., Endres, M., Babnigg, G., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.223 (Depositor), 0.233 (DCC) 
• R-Value Work: 
  0.187 (Depositor) 
• R-Value Observed: 
  0.189 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of the Beta Lactamase Class D YbxI from Agrobacterium fabrum

Kim, Y., Welk, L., Endres, M., Babnigg, G., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 4-mer - A4 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 112.08 kDa 
• Atom Count: 7,750 
• Modeled Residue Count: 974 
• Deposited Residue Count: 1,008 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase	A, B, C, D	252	Agrobacterium fabrum str. C58	Mutation(s): 0  Gene Names: Atu0933 EC: 3.5.2.6
UniProt
Find proteins for Q7D0B8 (Agrobacterium fabrum (strain C58 / ATCC 33970)) Explore Q7D0B8  Go to UniProtKB:  Q7D0B8

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	F [auth B], I [auth C]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL	E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	G [auth B], H [auth B], J [auth C], K [auth D]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.223 (Depositor), 0.233 (DCC) 
• R-Value Work:  0.187 (Depositor) 
• R-Value Observed: 0.189 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.879	α = 90
b = 165.957	β = 90.02
c = 75.428	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-01-16 
Deposition Author(s): Kim, Y., Welk, L., Endres, M., Babnigg, G., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	--

Revision History  

• Version 1.0: 2019-01-16
  Type: Initial release
  
• Version 1.1: 2019-12-18
  Changes: Author supporting evidence
• Version 1.2: 2023-10-11
  Changes: Data collection, Database references, Refinement description