5DAR

CRYSTAL STRUCTURE OF THE BASE OF THE RIBOSOMAL P STALK FROM METHANOCOCCUS JANNASCHII

• PDB DOI: https://doi.org/10.2210/pdb5DAR/pdb
• NAKB: 5DAR

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


• Deposited: 2015-08-20 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: 2.90 Å
• R-Value Free: 0.297 
• R-Value Work: 0.264 
• R-Value Observed: 0.266 

Literature

CRYSTAL STRUCTURE OF THE BASE OF THE RIBOSOMAL P STALK FROM METHANOCOCCUS JANNASCHII

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

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content

• Total Structure Weight: 130.09 kDa 
• Atom Count: 8,414 
• Modelled Residue Count: 829 
• Deposited Residue Count: 896 
• Unique protein chains: 2
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L10	B, E	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: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L11	C, F	161	Methanocaldococcus jannaschii	Mutation(s): 0  Gene Names: rpl11, MJ0373
UniProt
Find proteins for P54030 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)) Explore P54030  Go to UniProtKB:  P54030

Entity ID: 1
Molecule	Chains	Length	Organism	Image
74 nt fragment of 23S rRNA	A, D	74	Methanocaldococcus jannaschii

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
K	M [auth A], N [auth A], P [auth C], T [auth D], V [auth F]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL	L [auth A], O [auth B], U [auth F]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], Q [auth D], R [auth D], S [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.297 
• R-Value Work: 0.264 
• R-Value Observed: 0.266 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.396	α = 90
b = 88.451	β = 102.19
c = 95.231	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PROTEUM PLUS	data reduction
PROTEUM PLUS	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