5D6G | pdb_00005d6g

CRYSTAL STRUCTURE OF FRAGMENT OF RIBOSOMAL PROTEIN P0 IN COMPLEX WITH 74NT 23S RNA FROM METHANOCOCCUS JANNASCHII

• PDB DOI: https://doi.org/10.2210/pdb5D6G/pdb
• NAKB: 5D6G

• Classification: TRANSLATION
• Organism(s): Methanocaldococcus jannaschii
• Expression System: Escherichia coli BL21(DE3), Escherichia coli
• Mutation(s): No 


• Deposited: 2015-08-12 Released: 2016-09-14 
• Deposition Author(s): Gabdulkhakov, A.G., Mitroshin, I.V., Garber, M.B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free: 
  0.298 (Depositor), 0.310 (DCC) 
• R-Value Work: 
  0.245 (Depositor), 0.250 (DCC) 
• R-Value Observed: 
  0.247 (Depositor) 

Starting Model: experimental

Literature

CRYSTAL STRUCTURE OF FRAGMENT OF RIBOSOMAL PROTEIN P0 IN COMPLEX WITH 74NT 23S RNA FROM METHANOCOCCUS JANNASCHII

Gabdulkhakov, A.G., Mitroshin, I.V., Garber, M.B.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 47.33 kDa 
• Atom Count: 3,167 
• Modeled Residue Count: 279 
• Deposited Residue Count: 287 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L10	A	213	Methanocaldococcus jannaschii	Mutation(s): 0  Gene Names: rpl10, rplP0, MJ0509
UniProt
Find proteins for P54049 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)) Explore P54049  Go to UniProtKB:  P54049

Entity ID: 2
Molecule	Chains	Length	Organism	Image
23S ribosomal RNA	B [auth 0]	74	Methanocaldococcus jannaschii

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	C [auth 0], D [auth 0]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free:  0.298 (Depositor), 0.310 (DCC) 
• R-Value Work:  0.245 (Depositor), 0.250 (DCC) 
• R-Value Observed: 0.247 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.23	α = 90
b = 108.31	β = 90
c = 112.95	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-09-14 
Deposition Author(s): Gabdulkhakov, A.G., Mitroshin, I.V., Garber, M.B.

Revision History  

• Version 1.0: 2016-09-14
  Type: Initial release
  
• Version 1.1: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Refinement description