5K73

as-isolated Dbr1 with Fe(II) and Zn(II)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.08 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.180 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

The RNA lariat debranching enzyme Dbr1: metal dependence and branched RNA co-crystal structures

Clark, N.E.Katolik, A.Roberts, K.Taylor, A.B.Holloway, S.P.Schuermann, J.P.Montemayor, E.J.Stevens, S.W.Fitzpatrick, P.F.Damha, M.J.Hart, P.J.

(2016) Proc Natl Acad Sci U S A 


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RNA lariat debranching enzyme, putativeA, B, C, D, E356Entamoeba histolyticaMutation(s): 0 
Gene Names: EHI_062730
UniProt
Find proteins for C4M1P9 (Entamoeba histolytica)
Explore C4M1P9 
Go to UniProtKB:  C4M1P9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC4M1P9
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
AA [auth D],
BA [auth D],
CA [auth D],
GA [auth E],
H [auth A],
AA [auth D],
BA [auth D],
CA [auth D],
GA [auth E],
H [auth A],
I [auth A],
J [auth A],
N [auth B],
O [auth B],
P [auth B],
R [auth C],
U [auth C],
V [auth C],
Z [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
FA [auth E],
G [auth A],
M [auth B],
T [auth C],
Y [auth D]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
FE2
Query on FE2

Download Ideal Coordinates CCD File 
EA [auth E],
F [auth A],
L [auth B],
S [auth C],
X [auth D]
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
 Ligand Interaction
OH
Query on OH

Download Ideal Coordinates CCD File 
DA [auth D],
HA [auth E],
K [auth A],
Q [auth B],
W [auth C]
HYDROXIDE ION
H O
XLYOFNOQVPJJNP-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.08 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.180 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.161α = 90
b = 141.705β = 90
c = 213.777γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-12-07
    Type: Initial release
  • Version 1.1: 2017-09-27
    Changes: Author supporting evidence, Database references