6MIK

Crystal structure of host-guest complex with PP hachimoji DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.213 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Hachimoji DNA and RNA: A genetic system with eight building blocks.

Hoshika, S.Leal, N.A.Kim, M.J.Kim, M.S.Karalkar, N.B.Kim, H.J.Bates, A.M.Watkins Jr., N.E.SantaLucia, H.A.Meyer, A.J.DasGupta, S.Piccirilli, J.A.Ellington, A.D.SantaLucia Jr., J.Georgiadis, M.M.Benner, S.A.

(2019) Science 363: 884-887


Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
N-terminal fragment of MMLV reverse transcriptase
A
259Moloney murine leukemia virus (isolate Shinnick)Mutation(s): 0 
Gene Names: gag-pol
Find proteins for P03355 (Moloney murine leukemia virus (isolate Shinnick))
Go to UniProtKB:  P03355
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*TP*TP*AP*TP*(1WA)P*(1WA)P*(DS))-3')B8synthetic construct
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(P*(DB)P*(1W5)P*(1W5)P*AP*TP*AP*AP*G)-3')G8synthetic construct
Small Molecules
Modified Residues  4 Unique
IDChainsTypeFormula2D DiagramParent
1W5
Query on 1W5
G
DNA linkingC10 H14 N3 O9 P

--

1WA
Query on 1WA
B
DNA LINKINGC10 H16 N5 O7 P

--

IGU
Query on IGU
G
DNA LINKINGC10 H14 N5 O7 PDG
JSP
Query on JSP
B
DNA linkingC10 H16 N3 O7 P

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.213 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 55.152α = 90.00
b = 145.849β = 90.00
c = 46.849γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
PHASERphasing
XDSdata reduction
PDB_EXTRACTdata extraction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2018-09-19 
  • Released Date: 2019-02-27 
  • Deposition Author(s): Georgiadis, M.M.

Revision History 

  • Version 1.0: 2019-02-27
    Type: Initial release
  • Version 1.1: 2019-03-06
    Type: Data collection, Database references