3CTV | pdb_00003ctv

Crystal structure of central domain of 3-hydroxyacyl-CoA dehydrogenase from Archaeoglobus fulgidus

• PDB DOI: https://doi.org/10.2210/pdb3CTV/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Archaeoglobus fulgidus DSM 4304
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2008-04-14 Released: 2008-04-29 
• Deposition Author(s): Osipiuk, J., Evdokimova, E., Kudritska, M., Savchenko, A., Edwards, A.M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.46 Å
• R-Value Free: 
  0.247 (Depositor), 0.241 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.198 (DCC) 

Literature

X-ray crystal structure of central domain of 3-hydroxyacyl-CoA dehydrogenase from Archaeoglobus fulgidus.

Osipiuk, J., Evdokimova, E., Kudritska, M., Savchenko, A., Edwards, A.M., Joachimiak, A.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 12.26 kDa 
• Atom Count: 729 
• Modeled Residue Count: 92 
• Deposited Residue Count: 110 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-hydroxyacyl-CoA dehydrogenase	A	110	Archaeoglobus fulgidus DSM 4304	Mutation(s): 0  Gene Names: AF_2273
UniProt
Find proteins for O28011 (Archaeoglobus fulgidus (strain ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16)) Explore O28011  Go to UniProtKB:  O28011

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.46 Å
• R-Value Free:  0.247 (Depositor), 0.241 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.198 (DCC) 

Space Group: I 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.464	α = 90
b = 101.464	β = 90
c = 101.464	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing
DENZO	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-04-29 
Deposition Author(s): Osipiuk, J., Evdokimova, E., Kudritska, M., Savchenko, A., Edwards, A.M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2008-04-29
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2019-07-24
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.4: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary