5IZN | pdb_00005izn

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

• PDB DOI: https://doi.org/10.2210/pdb5IZN/pdb

• Classification: RIBOSOMAL PROTEIN
• Organism(s): Vibrio vulnificus CMCP6
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-03-25 Released: 2016-04-06 
• Deposition Author(s): Tan, K., Zhou, M., Kwon, K., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 
  0.252 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.205 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.207 (Depositor) 

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.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 86.39 kDa 
• Atom Count: 5,852 
• Modeled Residue Count: 742 
• Deposited Residue Count: 760 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L25	A, B, C, D, E, F, G, H	95	Vibrio vulnificus CMCP6	Mutation(s): 0  Gene Names: rplY, VV1_2850
UniProt
Find proteins for Q8D8W6 (Vibrio vulnificus (strain CMCP6)) Explore Q8D8W6  Go to UniProtKB:  Q8D8W6

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	I [auth A], J [auth B], K [auth B], L [auth C], M [auth D], N [auth E], O [auth F], P [auth H]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C, D, E, F, G, H	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free:  0.252 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.205 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.207 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m35izn

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 128.451	α = 90
b = 58.797	β = 90.51
c = 122.004	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	phasing
HKL-3000	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-04-06 
Deposition Author(s): Tan, K., Zhou, M., Kwon, K., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	HHSN272201200026C

Revision History  

• Version 1.0: 2016-04-06
  Type: Initial release
  
• Version 1.1: 2016-09-21
  Changes: Structure summary
• Version 1.2: 2017-09-20
  Changes: Author supporting evidence, Derived calculations, Refinement description
• Version 1.3: 2019-12-11
  Changes: Author supporting evidence
• Version 1.4: 2024-10-09
  Changes: Data collection, Database references, Structure summary