6NLW

The crystal structure of class D carbapenem-hydrolyzing beta-lactamase BlaA from Shewanella oneidensis MR-1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.185 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The crystal structure of class D carbapenem-hydrolyzing beta-lactamase BlaA from Shewanella oneidensis MR-1

Tan, K.Tesar, C.Endres, M.Joachimiak, A.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-lactamase
A, B, C, D
246Shewanella oneidensisMutation(s): 0 
Gene Names: blaOXA-54
EC: 3.5.2.6
UniProt
Find proteins for Q6RFZ0 (Shewanella oneidensis)
Explore Q6RFZ0 
Go to UniProtKB:  Q6RFZ0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6RFZ0
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PEG
Query on PEG

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EA [auth B]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
MLA
Query on MLA

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ZA [auth D]MALONIC ACID
C3 H4 O4
OFOBLEOULBTSOW-UHFFFAOYSA-N
SO4
Query on SO4

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G [auth A]
GA [auth C]
H [auth A]
HA [auth C]
I [auth A]
G [auth A],
GA [auth C],
H [auth A],
HA [auth C],
I [auth A],
IA [auth C],
J [auth A],
JA [auth C],
K [auth A],
L [auth A],
M [auth A],
PA [auth D],
QA [auth D],
RA [auth D],
SA [auth D],
T [auth B],
TA [auth D],
U [auth B],
UA [auth D],
V [auth B],
VA [auth D],
W [auth B],
WA [auth D],
X [auth B],
Y [auth B],
Z [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

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E [auth A],
F [auth A],
FA [auth C],
OA [auth D],
S [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
FMT
Query on FMT

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CA [auth B]
DA [auth B]
MA [auth C]
NA [auth C]
O [auth A]
CA [auth B],
DA [auth B],
MA [auth C],
NA [auth C],
O [auth A],
P [auth A],
Q [auth A],
R [auth A],
YA [auth D]
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
CL
Query on CL

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AA [auth B]
BA [auth B]
KA [auth C]
LA [auth C]
N [auth A]
AA [auth B],
BA [auth B],
KA [auth C],
LA [auth C],
N [auth A],
XA [auth D]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.185 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 174.333α = 90
b = 61.391β = 119.53
c = 122.802γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesHHSN272201700060C

Revision History  (Full details and data files)

  • Version 1.0: 2019-01-23
    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