5DAR | pdb_00005dar

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free:
0.297 (Depositor), 0.257 (DCC)
R-Value Work:
0.264 (Depositor)
R-Value Observed:
0.266 (Depositor)

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

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.

Macromolecule Content

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

Macromolecules

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| 3D Structure

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 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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| 3D Structure

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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P54030
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff)

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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
K Query on K Download:Ideal Coordinates CCD File SDF format, chain V [auth F] SDF format, chain T [auth D] SDF format, chain P [auth C] SDF format, chain N [auth A] SDF format, chain M [auth A] MOL2 format, chain V [auth F] MOL2 format, chain T [auth D] MOL2 format, chain P [auth C] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] mmCIF format, chain V [auth F] mmCIF format, chain T [auth D] mmCIF format, chain P [auth C] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A]	M [auth A], N [auth A], P [auth C], T [auth D], V [auth F]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain M [auth A] Focus chain N [auth A] Focus chain P [auth C] Focus chain T [auth D] Focus chain V [auth F] Interactions & Density Focus chain M [auth A] Focus chain N [auth A] Focus chain P [auth C] Focus chain T [auth D] Focus chain V [auth F]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain U [auth F] SDF format, chain O [auth B] SDF format, chain L [auth A] MOL2 format, chain U [auth F] MOL2 format, chain O [auth B] MOL2 format, chain L [auth A] mmCIF format, chain U [auth F] mmCIF format, chain O [auth B] mmCIF format, chain L [auth A]	L [auth A], O [auth B], U [auth F]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain L [auth A] Focus chain O [auth B] Focus chain U [auth F] Interactions & Density Focus chain L [auth A] Focus chain O [auth B] Focus chain U [auth F]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain S [auth D] SDF format, chain R [auth D] SDF format, chain Q [auth D] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain S [auth D] MOL2 format, chain R [auth D] MOL2 format, chain Q [auth D] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain S [auth D] mmCIF format, chain R [auth D] mmCIF format, chain Q [auth D] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	G [auth A] H [auth A] I [auth A] J [auth A] K [auth A] 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		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain Q [auth D] Focus chain R [auth D] Focus chain S [auth D] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain Q [auth D] Focus chain R [auth D] Focus chain S [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.297 (Depositor), 0.257 (DCC)
R-Value Work: 0.264 (Depositor)
R-Value Observed: 0.266 (Depositor)

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

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Entry History

Deposition Data

Released Date: 2016-09-14

Deposition Author(s):

Gabdulkhakov, A.G.

Mitroshin, I.V.

Garber, M.B.

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