7YN1 | pdb_00007yn1

Crystal structure of selenomethionine labeled CcbD

• PDB DOI: https://doi.org/10.2210/pdb7YN1/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., Kadlcik, S., Abe, I.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.240 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.203 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.204 (Depositor) 

Literature

Crystal structure of selenomethionine labeled CcbD

Mori, T., Kadlcik, S., Abe, I.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 164.35 kDa 
• Atom Count: 10,926 
• Modeled Residue Count: 1,389 
• Deposited Residue Count: 1,480 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CcbD	A, B, C, D	370	Streptomyces caelestis	Mutation(s): 0  Gene Names: HDA41_002772
UniProt
Find proteins for E9JES9 (Streptomyces caelestis) Explore E9JES9  Go to UniProtKB:  E9JES9

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C, D	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.240 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.203 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.204 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.683	α = 90.273
b = 90.932	β = 103.671
c = 98.563	γ = 90.194

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
CRANK2	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-08-02 
Deposition Author(s): Mori, T., Kadlcik, S., Abe, I.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2023-08-02
  Type: Initial release
  
• Version 1.1: 2024-11-20
  Changes: Data collection, Structure summary