5D8H | pdb_00005d8h

CRYSTAL STRUCTURE OF THE BASE OF THE RIBOSOMAL P STALK FROM METHANOCOCCUS JANNASCHII WITH ANTIBIOTIC THIOSTREPTON

PDB DOI: https://doi.org/10.2210/pdb5D8H/pdb
NAKB: 5D8H

Classification: RIBOSOMAL PROTEIN
Organism(s): Methanocaldococcus jannaschii, Streptomyces azureus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2015-08-17 Released: 2016-08-24
Deposition Author(s): Gabdulkhakov, A.G., Mitroshin, I.V., Garber, M.B.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.245 (Depositor), 0.240 (DCC)
R-Value Work:
0.208 (Depositor)
R-Value Observed:
0.210 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 2.1 of the entry. See complete history.

Literature

CRYSTAL STRUCTURE OF THE BASE OF THE RIBOSOMAL P STALK FROM METHANOCOCCUS JANNASCHII WITH ANTIBIOTIC THIOSTREPTON

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

To be published.

Macromolecule Content

Total Structure Weight: 67.89 kDa
Atom Count: 4,592
Modeled Residue Count: 458
Deposited Residue Count: 467
Unique protein chains: 3
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	213	Methanocaldococcus jannaschii	Mutation(s): 1 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	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

Find similar proteins by: Sequence | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
THIOSTREPTON	D	19	Streptomyces azureus	Mutation(s): 0
UniProt
Find proteins for P0C8P8 (Streptomyces azureus) Explore P0C8P8 Go to UniProtKB: P0C8P8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0C8P8
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff)

Molecule	Chains	Length	Organism
Entity ID: 1
23S ribosomal RNA	A	74	Methanocaldococcus jannaschii
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TRS Query on TRS Download:Ideal Coordinates CCD File SDF format, chain R [auth A] SDF format, chain S [auth A] SDF format, chain U [auth B] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] MOL2 format, chain U [auth B] mmCIF format, chain R [auth A] mmCIF format, chain S [auth A] mmCIF format, chain U [auth B]	R [auth A], S [auth A], U [auth B]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain R [auth A] Focus chain S [auth A] Focus chain U [auth B] Interactions & Density Focus chain R [auth A] Focus chain S [auth A] Focus chain U [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain V [auth C] SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain G [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain V [auth C] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain G [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain V [auth C] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain G [auth A]	E [auth A] F [auth A] G [auth A] H [auth A] I [auth A] E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], V [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] 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 L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain V [auth C] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] 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 L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain V [auth C]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain T [auth B] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain T [auth B] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain T [auth B]	O [auth A], P [auth A], Q [auth A], T [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain T [auth B] Interactions & Density Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain T [auth B]

Modified Residues 5 Unique
ID	Chains	Modified Residue	Modification Type	Formula	2D Diagram
MSE Query on MSE	B, C	MET	Selenomethionine	C₅ H₁₁ N O₂ Se
DHA Query on DHA	D	SER	Dehydroamino acid	C₃ H₅ N O₂
DBU Query on DBU	D	THR	Dehydroamino acid	C₄ H₇ N O₂
TS9 Query on TS9	D	ILE	Hydroxylation	C₆ H₁₃ N O₄
MH6 Query on MH6	D	SER	Dehydrogenation	C₃ H₅ N O₃

Non-standard Monomers 2 Unique
ID	Chains	Type	Formula	2D Diagram
BB9 Query on BB9	D	PEPTIDE LINKING	C₃ H₅ N O₂ S
DCY Query on DCY	D	D-PEPTIDE LINKING	C₃ H₇ N O₂ S

Biologically Interesting Molecules (External Reference)

1 Unique

Entity ID: 4
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000223 Query on PRD_000223	D	THIOSTREPTON	Thiopeptide / Antibiotic		Interactions Focus chain D Interactions & Density Focus chain D

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.245 (Depositor), 0.240 (DCC)
R-Value Work: 0.208 (Depositor)
R-Value Observed: 0.210 (Depositor)

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 125.07	α = 90
b = 127.16	β = 90
c = 132.93	γ = 90

Software Package:

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

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2016-08-24

Deposition Author(s):

Gabdulkhakov, A.G.

Mitroshin, I.V.

Garber, M.B.

Revision History (Full details and data files)

Version 1.0: 2016-08-24
Type: Initial release
Version 1.1: 2016-12-14
Changes: Structure summary
Version 1.2: 2016-12-21
Changes: Non-polymer description
Version 1.3: 2019-04-10
Changes: Advisory, Data collection, Database references
Version 2.0: 2019-04-24
Changes: Data collection, Polymer sequence
Version 2.1: 2025-04-09
Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary