2C9H | pdb_00002c9h

Structure of mitochondrial beta-ketoacyl synthase

• PDB DOI: https://doi.org/10.2210/pdb2C9H/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2005-12-12 Released: 2005-12-13 
• Deposition Author(s): Bunkoczi, G., Wu, X., Smee, C., Gileadi, O., Arrowsmith, C., Edwards, A., Sundstrom, M., Weigelt, J., von Delft, F., Oppermann, U.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.240 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.177 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.181 (Depositor) 

Starting Model: experimental

Literature

Structure of Mitochondrial Beta-Ketoacyl Synthase

Bunkoczi, G., Wu, X., Smee, C., Gileadi, O., Arrowsmith, C., Edwards, A., Sundstrom, M., Weigelt, J., von Delft, F., Oppermann, U.

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 PQS (software)

Macromolecule Content 

• Total Structure Weight: 47.27 kDa 
• Atom Count: 3,373 
• Modeled Residue Count: 427 
• Deposited Residue Count: 444 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MITOCHONDRIAL BETA-KETOACYL SYNTHASE	A	444	Homo sapiens	Mutation(s): 0  EC: 2.3.1.41
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NWU1 (Homo sapiens) Explore Q9NWU1  Go to UniProtKB:  Q9NWU1
PHAROS:  Q9NWU1 GTEx:  ENSG00000151093

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NI	B [auth A]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSD	A	L-PEPTIDE LINKING	C3 H7 N O4 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.240 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.177 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.181 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 116.725	α = 90
b = 58.056	β = 90
c = 58.987	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-12-13 
Deposition Author(s): Bunkoczi, G., Wu, X., Smee, C., Gileadi, O., Arrowsmith, C., Edwards, A., Sundstrom, M., Weigelt, J., von Delft, F., Oppermann, U.

Revision History  

• Version 1.0: 2005-12-13
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2018-01-24
  Changes: Database references, Structure summary
• Version 1.3: 2018-02-28
  Changes: Source and taxonomy
• Version 1.4: 2023-12-13
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description
• Version 1.5: 2024-11-13
  Changes: Structure summary