3K6J

Crystal structure of the dehydrogenase part of multifuctional enzyme 1 from C.elegans

• PDB DOI: https://doi.org/10.2210/pdb3K6J/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Caenorhabditis elegans
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-10-09 Released: 2010-10-13 
• Deposition Author(s): Ouyang, Z., Zhang, K., Zhai, Y., Lu, J., Sun, F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.267 
• R-Value Work: 0.210 
• R-Value Observed: 0.213 

Starting Model: experimental

Literature

Crystal structure of the dehydrogenase part of multifuctional enzyme 1 from C.elegans

Ouyang, Z., Zhang, K., Zhai, Y., Lu, J., Sun, F.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 52.69 kDa 
• Atom Count: 3,633 
• Modelled Residue Count: 430 
• Deposited Residue Count: 460 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein F01G10.3, confirmed by transcript evidence	A	460	Caenorhabditis elegans	Mutation(s): 0  Gene Names: ech-9, F01G10.3
UniProt
Find proteins for O17762 (Caenorhabditis elegans) Explore O17762  Go to UniProtKB:  O17762

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	B [auth A], C [auth A], D [auth A], E [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
ZN	F [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.267 
• R-Value Work: 0.210 
• R-Value Observed: 0.213 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.025	α = 90
b = 90.657	β = 90
c = 66.206	γ = 90

Software Package:

Software Name	Purpose
MAR345	data collection
PHASER	phasing
OASIS	model building
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
OASIS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-10-13 
Deposition Author(s): Ouyang, Z., Zhang, K., Zhai, Y., Lu, J., Sun, F.

Revision History  

• Version 1.0: 2010-10-13
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description