3MD7

Crystal structure of a beta-lactamase-like protein bound to GMP from brucella melitensis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.27 Å
  • R-Value Free: 0.134 
  • R-Value Work: 0.107 
  • R-Value Observed: 0.108 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

BrabA.11339.a: anomalous diffraction and ligand binding guide towards the elucidation of the function of a `putative beta-lactamase-like protein from Brucella melitensis.

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: 10.1107/S1744309111010220
  • Primary Citation of Related Structures:  
    3PY5, 3PY6, 3QH8, 3MD7

  • 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 e ...

    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)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-lactamase-likeA293Brucella abortus 2308Mutation(s): 0 
Gene Names: 3787676BAB1_1016
Find proteins for Q2YQ74 (Brucella abortus (strain 2308))
Explore Q2YQ74 
Go to UniProtKB:  Q2YQ74
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
5GP
Query on 5GP

Download CCD File 
A
GUANOSINE-5'-MONOPHOSPHATE
C10 H14 N5 O8 P
RQFCJASXJCIDSX-UUOKFMHZSA-N
 Ligand Interaction
TLA
Query on TLA

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A
L(+)-TARTARIC ACID
C4 H6 O6
FEWJPZIEWOKRBE-JCYAYHJZSA-N
 Ligand Interaction
MN
Query on MN

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A
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
K
Query on K

Download CCD File 
A
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

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A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.89α = 90
b = 75.25β = 90
c = 98.36γ = 90
Software Package:
Software NamePurpose
BOSdata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-04-21
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2011-09-21
    Changes: Database references