3QH8

Crystal structure of a beta-lactamase-like protein bound to AMP from brucella melitensis, long wavelength synchrotron data

• PDB DOI: https://doi.org/10.2210/pdb3QH8/pdb

• Classification: HYDROLASE
• Organism(s): Brucella abortus 2308
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-01-25 Released: 2011-02-09 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.166 
• R-Value Work: 0.143 
• R-Value Observed: 0.145 

Starting Model: experimental

Literature

Crystal structure of a Beta-Lactamase-Like Protein bound to AMP from Brucella Melitensis, long wavelength synchrotron data

Abendroth, J., Sankaran, B., Edwards, T.E., Gardberg, A.S., Dieterich, S., Bhandari, J., Napuli, A.J., Van Voorhis, W.C., Staker, B.L., Myler, P.J., Stewart, L.J.

(2011) Acta Crystallogr Sect F Struct Biol Cryst Commun 67: 1106-1112

• PubMed: 21904058 
• DOI: https://doi.org/10.1107/S1744309111010220
• Primary Citation of Related Structures:  
  3MD7, 3PY5, 3PY6, 3QH8


• PubMed Abstract: 
  

  The crystal structure of a β-lactamase-like protein from Brucella melitensis was initially solved by SAD phasing from an in-house data set collected on a crystal soaked with iodide. A high-resolution data set was collected at a synchroton at the Se edge wavelength, which also provided an independent source of phasing using a small anomalous signal from metal ions in the active site. Comparisons of anomalous peak heights at various wavelengths allowed the identification of the active-site metal ions as manganese. In the native data set a partially occupied GMP could be identified. When co-crystallized with AMPPNP or GMPPNP, clear density for the hydrolyzed analogs was observed, providing hints to the function of the protein.

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Organizational Affiliation: 

Seattle Structural Genomics Center for Infectious Disease (SSGCID), USA. [e-mail]

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: 31.43 kDa 
• Atom Count: 2,536 
• Modelled Residue Count: 272 
• Deposited Residue Count: 274 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase-like	A	274	Brucella abortus 2308	Mutation(s): 0  Gene Names: BAB1_1016
UniProt
Find proteins for Q2YQ74 (Brucella abortus (strain 2308)) Explore Q2YQ74  Go to UniProtKB:  Q2YQ74

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AMP	E [auth A]	ADENOSINE MONOPHOSPHATE C10 H14 N5 O7 P UDMBCSSLTHHNCD-KQYNXXCUSA-N
TLA	G [auth A]	L(+)-TARTARIC ACID C4 H6 O6 FEWJPZIEWOKRBE-JCYAYHJZSA-N
EDO	F [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
MN	B [auth A], C [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N
K	D [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.166 
• R-Value Work: 0.143 
• R-Value Observed: 0.145 
• Space Group: C 2 2 2₁
• Diffraction Data: https://doi.org/10.18430/M33QH8

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.21	α = 90
b = 75.53	β = 90
c = 98.94	γ = 90

Software Package:

Software Name	Purpose
BOS	data collection
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-02-09 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2011-02-09
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2011-09-21
  Changes: Database references
• Version 1.3: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description