3FWO | pdb_00003fwo

The large ribosomal subunit from Deinococcus radiodurans complexed with Methymycin

PDB DOI: https://doi.org/10.2210/pdb3FWO/pdb
NAKB: 3FWO

Classification: RIBOSOME
Organism(s): Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539
Mutation(s): No

Deposited: 2009-01-19 Released: 2010-01-19
Deposition Author(s): Auerbach, T., Mermershtain, I., Bashan, A., Davidovich, C., Rozenberg, H., Sherman, D.H., Yonath, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.71 Å
R-Value Free:
0.337 (Depositor), 0.386 (DCC)
R-Value Work:
0.278 (Depositor), 0.363 (DCC)
R-Value Observed:
0.278 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Structural basis for the antibacterial activity of the 12-membered-ring mono-sugar macrolide methymycin

Auerbach, T., Mermershtain, I., Bashan, A., Davidovich, C., Rozenberg, H., Sherman, D.H., Yonath, A.

(2009) BioTechnologia (Pozn) 1: 24-35

Macromolecule Content

Total Structure Weight: 971.9 kDa
Atom Count: 61,885
Modeled Residue Count: 2,883
Deposited Residue Count: 2,998
Unique nucleic acid chains: 2

Macromolecules

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(by identity cutoff)

Molecule	Chains	Length	Organism
Entity ID: 1
23S RIBOSOMAL RNA	A	2,880	Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff)

Molecule	Chains	Length	Organism
Entity ID: 2
5S RIBOSOMAL RNA	B	118	Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MT9 Query on MT9 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	(3R,4S,5S,7R,9E,11S,12R)-12-ethyl-11-hydroxy-3,5,7,11-tetramethyl-2,8-dioxooxacyclododec-9-en-4-yl 3,4,6-trideoxy-3-(dimethylamino)-beta-D-xylo-hexopyranoside C₂₅ H₄₃ N O₇ HUKYPYXOBINMND-HYUJHOPRSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.71 Å
R-Value Free: 0.337 (Depositor), 0.386 (DCC)
R-Value Work: 0.278 (Depositor), 0.363 (DCC)
R-Value Observed: 0.278 (Depositor)

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 172.499	α = 90
b = 415.691	β = 90
c = 701.729	γ = 90

Software Package:

Software Name	Purpose
MxCuBE	data collection
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2010-01-19

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2010-01-19
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2014-02-19
Changes: Database references, Structure summary
Version 1.3: 2024-02-21
Changes: Data collection, Database references, Derived calculations