3SHD

Crystal structure of Nudix hydrolase Orf153, ymfB, from Escherichia coli K-1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.230 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Structure and atypical hydrolysis mechanism of the Nudix hydrolase Orf153 (YmfB) from Escherichia coli

Hong, M.K.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Phosphatase nudJ
A, B, C, D, E, F, G, H, I, J, K, L
A, B, C, D, E, F, G, H, I, J, K, L
153Escherichia coli APEC O1Mutation(s): 0 
Gene Names: nudJEcok1_10240APECO1_216
EC: 3.6.1
UniProt
Find proteins for A1AA28 (Escherichia coli O1:K1 / APEC)
Explore A1AA28 
Go to UniProtKB:  A1AA28
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA1AA28
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
AA [auth C],
CB [auth I],
DA [auth D],
DB [auth I],
EA [auth D],
AA [auth C],
CB [auth I],
DA [auth D],
DB [auth I],
EA [auth D],
EB [auth I],
FA [auth D],
HB [auth J],
IA [auth E],
IB [auth J],
JA [auth E],
JB [auth J],
KA [auth E],
MB [auth K],
NA [auth F],
NB [auth K],
O [auth A],
OA [auth F],
OB [auth K],
P [auth A],
PA [auth F],
Q [auth A],
RB [auth L],
SA [auth G],
SB [auth L],
T [auth B],
TA [auth G],
TB [auth L],
U [auth B],
UA [auth G],
V [auth B],
XA [auth H],
Y [auth C],
YA [auth H],
Z [auth C],
ZA [auth H]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
MN
Query on MN

Download Ideal Coordinates CCD File 
AB [auth I],
BA [auth D],
BB [auth I],
CA [auth D],
FB [auth J],
AB [auth I],
BA [auth D],
BB [auth I],
CA [auth D],
FB [auth J],
GA [auth E],
GB [auth J],
HA [auth E],
KB [auth K],
LA [auth F],
LB [auth K],
M [auth A],
MA [auth F],
N [auth A],
PB [auth L],
QA [auth G],
QB [auth L],
R [auth B],
RA [auth G],
S [auth B],
VA [auth H],
W [auth C],
WA [auth H],
X [auth C]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.230 
  • Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 111.126α = 90
b = 111.126β = 90
c = 247.306γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASESphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-06-27
    Type: Initial release