4DZ4

X-ray crystal structure of a hypothetical Agmatinase from Burkholderia thailandensis

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.152 
  • R-Value Observed: 0.154 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Combining functional and structural genomics to sample the essential Burkholderia structome.

Baugh, L., Gallagher, L.A., Patrapuvich, R., Clifton, M.C., Gardberg, A.S., Edwards, T.E., Armour, B., Begley, D.W., Dieterich, S.H., Dranow, D.M., Abendroth, J., Fairman, J.W., Fox, D., Staker, B.L., Phan, I., Gillespie, A., Choi, R., Nakazawa-Hewitt, S., Nguyen, M.T., Napuli, A., Barrett, L., Buchko, G.W., Stacy, R., Myler, P.J., Stewart, L.J., Manoil, C., Van Voorhis, W.C.

(2013) PLoS One 8: e53851-e53851

  • DOI: https://doi.org/10.1371/journal.pone.0053851
  • Primary Citation of Related Structures:  
    3D63, 3DAH, 3EIZ, 3EJ2, 3EK2, 3EZO, 3F0F, 3FTP, 3GK0, 3GK3, 3GVF, 3GWA, 3GWE, 3IML, 3SZ8, 3T4C, 3TML, 3TMQ, 3TXY, 3U7J, 3UE9, 3UK1, 3UK2, 3UND, 3UPT, 3URR, 3UW1, 3UW2, 3UW3, 3V2I, 3V7N, 3V8H, 3V9O, 3V9P, 3VAV, 4DDO, 4DFE, 4DHE, 4DHK, 4DUT, 4DZ4, 4E4T, 4EFI, 4EG0, 4EGJ, 4EK2, 4EQY, 4EWG, 4EXQ, 4F2G

  • PubMed Abstract: 

    • The genus Burkholderia includes pathogenic gram-negative bacteria that cause melioidosis, glanders, and pulmonary infections of patients with cancer and cystic fibrosis. Drug resistance has made development of new antimicrobials critical. Many approaches to discovering new antimicrobials, such as structure-based drug design and whole cell phenotypic screens followed by lead refinement, require high-resolution structures of proteins essential to the parasite ...

    The genus Burkholderia includes pathogenic gram-negative bacteria that cause melioidosis, glanders, and pulmonary infections of patients with cancer and cystic fibrosis. Drug resistance has made development of new antimicrobials critical. Many approaches to discovering new antimicrobials, such as structure-based drug design and whole cell phenotypic screens followed by lead refinement, require high-resolution structures of proteins essential to the parasite.

    Organizational Affiliation: 

    Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington, United States of America.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Agmatinase
A, B, C, D, E
A, B, C, D, E, F
324Burkholderia thailandensis E264Mutation(s): 0 
Gene Names: BTH_II1941
EC: 3.5.3.11
UniProt
Find proteins for Q2T3W4 (Burkholderia thailandensis (strain ATCC 700388 / DSM 13276 / CIP 106301 / E264))
Explore Q2T3W4 
Go to UniProtKB:  Q2T3W4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2T3W4
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
UNK
Query on UNK
Download Ideal Coordinates CCD File 
AB [auth D]
AC [auth F]
BA [auth B]
BB [auth D]
CA [auth B]
AB [auth D],
AC [auth F],
BA [auth B],
BB [auth D],
CA [auth B],
M [auth A],
N [auth A],
NA [auth C],
NB [auth E],
O [auth A],
OA [auth C],
OB [auth E],
ZA [auth D],
ZB [auth F]
UNKNOWN
C4 H9 N O2
QWCKQJZIFLGMSD-VKHMYHEASA-N		 Ligand Interaction
EDO
Query on EDO
Download Ideal Coordinates CCD File 
AA [auth B]
EB [auth E]
FA [auth C]
FB [auth E]
GA [auth C]
AA [auth B],
EB [auth E],
FA [auth C],
FB [auth E],
GA [auth C],
GB [auth E],
HA [auth C],
HB [auth E],
I [auth A],
IA [auth C],
IB [auth E],
J [auth A],
JA [auth C],
JB [auth E],
K [auth A],
KA [auth C],
KB [auth E],
L [auth A],
LA [auth C],
LB [auth E],
MA [auth C],
MB [auth E],
R [auth B],
RA [auth D],
RB [auth F],
S [auth B],
SA [auth D],
SB [auth F],
T [auth B],
TA [auth D],
TB [auth F],
U [auth B],
UA [auth D],
UB [auth F],
V [auth B],
VA [auth D],
VB [auth F],
W [auth B],
WA [auth D],
WB [auth F],
X [auth B],
XA [auth D],
XB [auth F],
Y [auth B],
YA [auth D],
YB [auth F],
Z [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N		 Ligand Interaction
MN
Query on MN
Download Ideal Coordinates CCD File 
CB [auth E]
DA [auth C]
DB [auth E]
EA [auth C]
G [auth A]
CB [auth E],
DA [auth C],
DB [auth E],
EA [auth C],
G [auth A],
H [auth A],
P [auth B],
PA [auth D],
PB [auth F],
Q [auth B],
QA [auth D],
QB [auth F]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.08α = 90
b = 101.25β = 97.09
c = 102.99γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
JDirectordata collection
XDSdata reduction

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-03-28
    Type: Initial release
  • Version 1.1: 2013-10-30
    Changes: Database references