3PNZ

Crystal structure of the lactonase Lmo2620 from Listeria monocytogenes


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.179 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Crystal structure of the lactonase Lmo2620 from Listeria monocytogenes

Fedorov, A.A.Fedorov, E.V.Xiang, D.F.Raushel, F.M.Almo, S.C.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Phosphotriesterase family protein
A, B, C, D, E, F
A, B, C, D, E, F
330Listeria monocytogenes serotype 4b str. H7858Mutation(s): 0 
Gene Names: LMOh7858_2908
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download Ideal Coordinates CCD File 
DA [auth C],
EA [auth C],
FA [auth C],
FB [auth F],
GA [auth C],
DA [auth C],
EA [auth C],
FA [auth C],
FB [auth F],
GA [auth C],
GB [auth F],
HB [auth F],
K [auth A],
L [auth A],
M [auth A],
MA [auth D],
NA [auth D],
OA [auth D],
S [auth B],
T [auth B],
U [auth B],
VA [auth E],
WA [auth E],
XA [auth E],
YA [auth E],
ZA [auth E]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
AA [auth C],
AB [auth F],
BB [auth F],
CB [auth F],
G [auth A],
AA [auth C],
AB [auth F],
BB [auth F],
CB [auth F],
G [auth A],
H [auth A],
HA [auth D],
IA [auth D],
JA [auth D],
N [auth B],
O [auth B],
P [auth B],
PA [auth E],
QA [auth E],
RA [auth E],
SA [auth E],
V [auth C],
W [auth C],
X [auth C],
Y [auth C],
Z [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
BA [auth C],
CA [auth C],
DB [auth F],
EB [auth F],
I [auth A],
BA [auth C],
CA [auth C],
DB [auth F],
EB [auth F],
I [auth A],
J [auth A],
KA [auth D],
LA [auth D],
Q [auth B],
R [auth B],
TA [auth E],
UA [auth E]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
KCX
Query on KCX
A, B, C, D, E, F
A, B, C, D, E, F
L-PEPTIDE LINKINGC7 H14 N2 O4LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.179 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 152.723α = 90
b = 62.933β = 89.97
c = 152.744γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
BALBESphasing
PHENIXrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-11-23
    Type: Initial release