3QH8

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


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
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


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

  • 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.


  • Organizational Affiliation

    Seattle Structural Genomics Center for Infectious Disease (SSGCID), USA. jabendroth@embios.com


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-lactamase-like274Brucella abortus 2308Mutation(s): 0 
Gene Names: BAB1_1016
UniProt
Find proteins for Q2YQ74 (Brucella abortus (strain 2308))
Explore Q2YQ74 
Go to UniProtKB:  Q2YQ74
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2YQ74
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AMP
Query on AMP

Download Ideal Coordinates CCD File 
E [auth A]ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
TLA
Query on TLA

Download Ideal Coordinates CCD File 
G [auth A]L(+)-TARTARIC ACID
C4 H6 O6
FEWJPZIEWOKRBE-JCYAYHJZSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
F [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
MN
Query on MN

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
K
Query on K

Download Ideal Coordinates CCD File 
D [auth A]POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.21α = 90
b = 75.53β = 90
c = 98.94γ = 90
Software Package:
Software NamePurpose
BOSdata collection
REFMACrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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