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 1.2 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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence 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 / CCUG 48851 / CIP 106301 / E264))
Explore Q2T3W4 
Go to UniProtKB:  Q2T3W4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2T3W4
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / 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
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
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
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



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
  • Version 1.2: 2024-02-28
    Changes: Data collection, Database references, Derived calculations, Refinement description