5IZN

The crystal structure of 50S ribosomal protein L25 from Vibrio vulnificus CMCP6


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.205 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

The crystal structure of 50S ribosomal protein L25 from Vibrio vulnificus CMCP6

Tan, K.Zhou, M.Kwon, K.Anderson, W.F.Joachimiak, A.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L25
A, B, C, D, E, F, G, H
95Vibrio vulnificus (strain CMCP6)Mutation(s): 0 
Gene Names: rplY
Find proteins for Q8D8W6 (Vibrio vulnificus (strain CMCP6))
Go to UniProtKB:  Q8D8W6
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A, B, C, D, E, F, H
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D, E, F, G, H
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 128.451α = 90.00
b = 58.797β = 90.51
c = 122.004γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000phasing
HKL-3000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesHHSN272201200026C

Revision History 

  • Version 1.0: 2016-04-06
    Type: Initial release
  • Version 1.1: 2016-09-21
    Type: Structure summary
  • Version 1.2: 2017-09-20
    Type: Author supporting evidence, Derived calculations, Refinement description
  • Version 1.3: 2019-12-11
    Type: Author supporting evidence