2JB8 | pdb_00002jb8

Deacetoxycephalosporin C synthase complexed with 5-hydroxy-4-keto valeric acid

• PDB DOI: https://doi.org/10.2210/pdb2JB8/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Streptomyces clavuligerus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2006-12-05 Released: 2008-02-05 
• Deposition Author(s): Cicero, G., Carbonera, C., Valegard, K., Hajdu, J., Andersson, I., Ranghino, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.53 Å
• R-Value Free: 
  0.249 (Depositor), 0.242 (DCC) 
• R-Value Work: 
  0.210 (Depositor), 0.207 (DCC) 
• R-Value Observed: 
  0.212 (Depositor) 

Starting Model: experimental

Literature

Study of the Oxidative Half-Reaction Catalysed by a Non-Heme Ferrous Catalytic Centre by Means of Structural and Computational Methodologies

Cicero, G., Carbonera, C., Valegard, K., Hajdu, J., Andersson, I., Ranghino, G.

(2007) Int J Quantum Chem 107: 1514

• DOI: https://doi.org/10.1002/QUA.21275

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 34.78 kDa 
• Atom Count: 2,360 
• Modeled Residue Count: 273 
• Deposited Residue Count: 311 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DEACETOXYCEPHALOSPORIN C SYNTHETASE	A	311	Streptomyces clavuligerus	Mutation(s): 0  EC: 1.14.20.1
UniProt
Find proteins for P18548 (Streptomyces clavuligerus) Explore P18548  Go to UniProtKB:  P18548

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HKV	C [auth A]	4,5-DIOXOPENTANOIC ACID C5 H6 O4 YHUFRVYVNKGICT-UHFFFAOYSA-N
FE	B [auth A]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.53 Å
• R-Value Free:  0.249 (Depositor), 0.242 (DCC) 
• R-Value Work:  0.210 (Depositor), 0.207 (DCC) 
• R-Value Observed: 0.212 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.5	α = 90
b = 106.5	β = 90
c = 71.2	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-02-05 
Deposition Author(s): Cicero, G., Carbonera, C., Valegard, K., Hajdu, J., Andersson, I., Ranghino, G.

Revision History  

• Version 1.0: 2008-02-05
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2014-02-05
  Changes: Database references, Derived calculations, Other, Structure summary
• Version 1.3: 2023-12-13
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description