1E3U

MAD structure of OXA10 class D beta-lactamase

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.66 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.181 

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This is version 1.4 of the entry. See complete history. 


Literature

Insights Into Class D Beta-Lactamases are Revealed by the Crystal Structure of the Oxa10 Enzyme from Pseudomonas Aeruginosa

Maveyraud, L., Golemi, D., Kotra, L.P., Tranier, S., Vakulenko, S., Mobashery, S., Samama, J.P.

(2000) Structure 8: 1289

  • DOI: 10.1016/s0969-2126(00)00534-7
  • Primary Citation of Related Structures:  
    1E3U, 1E4D

  • PubMed Abstract: 

    • beta-lactam antibiotic therapies are commonly challenged by the hydrolytic activities of beta-lactamases in bacteria. These enzymes have been grouped into four classes: A, B, C, and D. Class B beta-lactamases are zinc dependent, and enzymes of classes A, C, and D are transiently acylated on a serine residue in the course of the turnover chemistry ...

    beta-lactam antibiotic therapies are commonly challenged by the hydrolytic activities of beta-lactamases in bacteria. These enzymes have been grouped into four classes: A, B, C, and D. Class B beta-lactamases are zinc dependent, and enzymes of classes A, C, and D are transiently acylated on a serine residue in the course of the turnover chemistry. While class A and C beta-lactamases have been extensively characterized by biochemical and structural methods, class D enzymes remain the least studied despite their increasing importance in the clinic.

    Organizational Affiliation: 

    Groupe de Cristallographie Biologique IPBS-CNRS, Toulouse, France.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
BETA-LACTAMASE OXA-10A, B, C246Pseudomonas aeruginosaMutation(s): 0 
Gene Names: bla, oxa10, pse2
EC: 3.5.2.6
UniProt
Find proteins for P14489 (Pseudomonas aeruginosa)
Explore P14489 
Go to UniProtKB:  P14489
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14489
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
BETA-LACTAMASE OXA-10D246Pseudomonas aeruginosaMutation(s): 0 
Gene Names: bla, oxa10, pse2
EC: 3.5.2.6
UniProt
Find proteins for P14489 (Pseudomonas aeruginosa)
Explore P14489 
Go to UniProtKB:  P14489
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14489
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AUC
Query on AUC
Download Ideal Coordinates CCD File 
AA [auth C],
E [auth A],
GA [auth D],
HA [auth D],
IA [auth D],
AA [auth C],
E [auth A],
GA [auth D],
HA [auth D],
IA [auth D],
N [auth B],
Y [auth C],
Z [auth C]
GOLD (I) CYANIDE ION
C2 Au N2
DGOHFTDNMSZWDQ-UHFFFAOYSA-N		 Ligand Interaction
SO4
Query on SO4
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BA [auth C],
CA [auth C],
F [auth A],
G [auth A],
H [auth A],
BA [auth C],
CA [auth C],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
JA [auth D],
K [auth A],
KA [auth D],
LA [auth D],
O [auth B],
P [auth B],
Q [auth B],
R [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
EDO
Query on EDO
Download Ideal Coordinates CCD File 
DA [auth C],
EA [auth C],
FA [auth C],
L [auth A],
M [auth A],
DA [auth C],
EA [auth C],
FA [auth C],
L [auth A],
M [auth A],
MA [auth D],
S [auth B],
T [auth B],
U [auth B],
V [auth B],
W [auth B],
X [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.66 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.181 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.53α = 90
b = 82.94β = 95.03
c = 101.42γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
SOLVEphasing
REFMACrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-01-12
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-07-12
    Changes: Derived calculations
  • Version 1.4: 2019-07-24
    Changes: Data collection