4R85

Crystal structure of 5-methylcytosine deaminase from Klebsiella pneumoniae liganded with 5-methylcytosine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.159 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Crystal structure of 5-methylcytosine deaminase from Klebsiella pneumoniae liganded with 5-methylcytosine

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

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cytosine deaminase
A, B, C, D, E, F
A, B, C, D, E, F
431Klebsiella pneumoniae 30660/NJST258_1Mutation(s): 0 
Gene Names: KPNJ1_03949
EC: 3.5.4.1
UniProt
Find proteins for A0A0E1CHI1 (Klebsiella pneumoniae 30660/NJST258_1)
Explore A0A0E1CHI1 
Go to UniProtKB:  A0A0E1CHI1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0E1CHI1
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
17E
Query on 17E

Download Ideal Coordinates CCD File 
AA [auth E],
G [auth A],
GA [auth F],
L [auth B],
R [auth C],
AA [auth E],
G [auth A],
GA [auth F],
L [auth B],
R [auth C],
W [auth D]
5-methylcytosine
C5 H7 N3 O
LRSASMSXMSNRBT-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
CA [auth E],
DA [auth E],
EA [auth E],
FA [auth F],
I [auth A],
CA [auth E],
DA [auth E],
EA [auth E],
FA [auth F],
I [auth A],
IA [auth F],
J [auth A],
JA [auth F],
K [auth A],
N [auth B],
O [auth B],
P [auth B],
Q [auth B],
T [auth C],
U [auth C],
V [auth C],
Y [auth D],
Z [auth D]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
FE2
Query on FE2

Download Ideal Coordinates CCD File 
BA [auth E],
H [auth A],
HA [auth F],
M [auth B],
S [auth C],
BA [auth E],
H [auth A],
HA [auth F],
M [auth B],
S [auth C],
X [auth D]
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.159 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 111.481α = 90
b = 137.669β = 118.03
c = 112.093γ = 90
Software Package:
Software NamePurpose
CBASSdata collection
BALBESphasing
PHENIXrefinement
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: 2014-09-17
    Type: Initial release