7YN2 | pdb_00007yn2

Crystal structure of CcbD with methylthiolincosamide

PDB DOI: https://doi.org/10.2210/pdb7YN2/pdb

Classification: LYASE
Organism(s): Streptomyces caelestis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-07-29 Released: 2023-08-02
Deposition Author(s): Mori, T., Lyu, S., Abe, I.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.238 (Depositor), 0.239 (DCC)
R-Value Work:
0.200 (Depositor), 0.200 (DCC)
R-Value Observed:
0.201 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of CcbD with methylthiolincosamide

Mori, T., Lyu, S., Abe, I.

To be published.

Macromolecule Content

Total Structure Weight: 80.95 kDa
Atom Count: 5,615
Modeled Residue Count: 695
Deposited Residue Count: 730
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CcbD	A, B	365	Streptomyces caelestis	Mutation(s): 0 Gene Names: HDA41_002772
UniProt
Find proteins for E9JES9 (Streptomyces caelestis) Explore E9JES9 Go to UniProtKB: E9JES9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	E9JES9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
IYV (Subject of Investigation/LOI) Query on IYV 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]	(2R,3R,4S,5R,6R)-2-[(1R,2R)-1-azanyl-2-oxidanyl-propyl]-6-methylsulfanyl-oxane-3,4,5-triol C₉ H₁₉ N O₅ S AEEIMWYSDWZKAT-HJTGYUAHSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.238 (Depositor), 0.239 (DCC)
R-Value Work: 0.200 (Depositor), 0.200 (DCC)
R-Value Observed: 0.201 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 192.059	α = 90
b = 52.903	β = 91.103
c = 90.938	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-08-02

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2023-08-02
Type: Initial release
Version 1.1: 2024-05-29
Changes: Data collection
Version 1.2: 2026-03-04
Changes: Refinement description, Structure summary

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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.