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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.30 Å
R-Value Free:
0.298 (Depositor), 0.305 (DCC)
R-Value Work:
0.245 (Depositor), 0.253 (DCC)
R-Value Observed:
0.247 (Depositor)

Starting Model: experimental
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This is version 1.1 of the entry. See complete history.

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.

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

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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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P54049
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff)

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain C [auth 0] SDF format, chain D [auth 0] MOL2 format, chain C [auth 0] MOL2 format, chain D [auth 0] mmCIF format, chain C [auth 0] mmCIF format, chain D [auth 0]	C [auth 0], D [auth 0]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth 0] Focus chain D [auth 0] Interactions & Density Focus chain C [auth 0] Focus chain D [auth 0]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.30 Å
R-Value Free: 0.298 (Depositor), 0.305 (DCC)
R-Value Work: 0.245 (Depositor), 0.253 (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

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Entry History

Deposition Data

Released Date: 2016-09-14

Deposition Author(s):

Gabdulkhakov, A.G.

Mitroshin, I.V.

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.