7YN3 | pdb_00007yn3

Crystal structure of CcbD complex with CcbZ carrier protein domain

• PDB DOI: https://doi.org/10.2210/pdb7YN3/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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.226 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.175 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.177 (Depositor) 

Literature

Crystal structure of CcbD complex with carrier protein

Mori, T., Lyu, S., Abe, I.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 99.79 kDa 
• Atom Count: 7,256 
• Modeled Residue Count: 844 
• Deposited Residue Count: 896 
• Unique protein chains: 2

Macromolecules

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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
CcbZ	C, D	78	Streptomyces caelestis	Mutation(s): 0  Gene Names: HDA41_002769
UniProt
Find proteins for E9JES6 (Streptomyces caelestis) Explore E9JES6  Go to UniProtKB:  E9JES6

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PNS (Subject of Investigation/LOI)	G [auth B], H [auth C]	4'-PHOSPHOPANTETHEINE C11 H23 N2 O7 P S JDMUPRLRUUMCTL-VIFPVBQESA-N
1N2 (Subject of Investigation/LOI)	E [auth A], F [auth B]	1,1'-ethane-1,2-diyldipyrrolidine-2,5-dione C10 H12 N2 O4 ZFMTZVFTWHQGNQ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.226 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.175 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.177 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.572	α = 90
b = 90.104	β = 90
c = 124.411	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-08-02 
Deposition Author(s): Mori, T., Lyu, 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