9DKS | pdb_00009dks

Crystal structure of CcbD C19S mutant complexed with single PCP domain of CcbZ

• PDB DOI: https://doi.org/10.2210/pdb9DKS/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Streptomyces caelestis
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2024-09-09 Released: 2025-09-17 
• Deposition Author(s): Heberlig, G.W., Podust, L.M., Burkart, M.D.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 
  0.205 (Depositor), 0.205 (DCC) 
• R-Value Work: 
  0.177 (Depositor), 0.177 (DCC) 

Starting Model: experimental

Literature

Crystal structure of CcbD complexed with PCP domain of CcbZ

Heberlig, G.W., Podust, L.M., Burkart, M.D.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 90.13 kDa 
• Atom Count: 6,683 
• Modeled Residue Count: 770 
• Deposited Residue Count: 818 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CcbD	A [auth B], B [auth A]	357	Streptomyces caelestis	Mutation(s): 1  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	104	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)	F [auth C]	4'-PHOSPHOPANTETHEINE C11 H23 N2 O7 P S JDMUPRLRUUMCTL-VIFPVBQESA-N
MLI	D [auth B], E [auth A]	MALONATE ION C3 H2 O4 OFOBLEOULBTSOW-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free:  0.205 (Depositor), 0.205 (DCC) 
• R-Value Work:  0.177 (Depositor), 0.177 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.28	α = 90
b = 89.079	β = 90
c = 135.029	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-09-17 
Deposition Author(s): Heberlig, G.W., Podust, L.M., Burkart, M.D.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM095970
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)	United States	K12HL141956

Revision History  

• Version 1.0: 2025-09-17
  Type: Initial release