5YHB

Crystal structure of Pd(allyl)/polyhedra mutant with deletion of Gly192-Ala194


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.08 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure of in cell protein crystals containing organometallic complexes.

Abe, S.Atsumi, K.Yamashita, K.Hirata, K.Mori, H.Ueno, T.

(2018) Phys Chem Chem Phys 20: 2986-2989

  • DOI: 10.1039/c7cp06651a
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The molecular structures of in cell protein crystals containing organometallic Pd(allyl) complexes were determined by performing microfocus X-ray diffraction experiments. The coordination sites in a polyhedrin mutant with deletion of selected amino a ...

    The molecular structures of in cell protein crystals containing organometallic Pd(allyl) complexes were determined by performing microfocus X-ray diffraction experiments. The coordination sites in a polyhedrin mutant with deletion of selected amino acid residues located at the interface of the polyhedrin trimer are dramatically altered compared to those of the wild-type composite.


    Organizational Affiliation

    School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan. saabe@bio.titech.ac.jp tueno@bio.titech.ac.jp.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Polyhedrin
A
245Bombyx mori cytoplasmic polyhedrosis virusMutation(s): 0 
Find proteins for P11041 (Bombyx mori cytoplasmic polyhedrosis virus)
Go to UniProtKB:  P11041
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PD
Query on PD

Download SDF File 
Download CCD File 
A
PALLADIUM ION
Pd
MUJIDPITZJWBSW-UHFFFAOYSA-N
 Ligand Interaction
PLL
Query on PLL

Download SDF File 
Download CCD File 
A
Palladium(II) allyl complex
C3 H5 Pd
WTWGCTVOVPTEEU-CPNWEVAQAE
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
ACE
Query on ACE
A
NON-POLYMERC2 H4 O

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.08 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.188 
  • Space Group: I 2 3
Unit Cell:
Length (Å)Angle (°)
a = 105.920α = 90.00
b = 105.920β = 90.00
c = 105.920γ = 90.00
Software Package:
Software NamePurpose
PHENIXphasing
REFMACrefinement
XSCALEdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of ScienceJapanJP16H00827

Revision History 

  • Version 1.0: 2017-11-29
    Type: Initial release
  • Version 1.1: 2018-02-14
    Type: Database references