4R7W

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.199 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

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

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
MoleculeChains Sequence LengthOrganismDetailsImage
Cytosine deaminase
A, B, C, D, E
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
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
O7U
Query on O7U

Download Ideal Coordinates CCD File 
DA [auth F]
H [auth A]
M [auth B]
P [auth C]
V [auth D]
DA [auth F],
H [auth A],
M [auth B],
P [auth C],
V [auth D],
Z [auth E]
(2R)-2-amino-2,5-dihydro-1,5,2-diazaphosphinin-6(1H)-one 2-oxide
C3 H6 N3 O2 P
GGLLBAYBJJLFCT-SECBINFHSA-N
PEG
Query on PEG

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BA [auth E],
I [auth A],
R [auth C],
S [auth C],
W [auth D]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL
Query on GOL

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Q [auth C]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO
Query on EDO

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AA [auth E]
J [auth A]
K [auth A]
N [auth B]
T [auth C]
AA [auth E],
J [auth A],
K [auth A],
N [auth B],
T [auth C],
X [auth D]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
FE2
Query on FE2

Download Ideal Coordinates CCD File 
CA [auth F]
G [auth A]
L [auth B]
O [auth C]
U [auth D]
CA [auth F],
G [auth A],
L [auth B],
O [auth C],
U [auth D],
Y [auth E]
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.199 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.167α = 90
b = 147.808β = 90
c = 185.336γ = 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
  • Version 1.1: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description