1WYB | pdb_00001wyb

Structure of 6-aminohexanoate-dimer hydrolase

• PDB DOI: https://doi.org/10.2210/pdb1WYB/pdb

• Classification: HYDROLASE
• Organism(s): Flavobacterium sp.
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2005-02-09 Released: 2005-09-20 
• Deposition Author(s): Negoro, S., Ohki, T., Shibata, N., Mizuno, N., Wakitani, Y., Tsurukame, J., Matsumoto, K., Kawamoto, I., Takeo, M., Higuchi, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.203 (Depositor), 0.203 (DCC) 
• R-Value Work: 
  0.185 (Depositor), 0.185 (DCC) 
• R-Value Observed: 
  0.185 (Depositor) 

Literature

Structure of 6-aminohexanoate-dimer hydrolase

Negoro, S., Ohki, T., Shibata, N., Mizuno, N., Wakitani, Y., Tsurukame, J., Matsumoto, K., Kawamoto, I., Takeo, M., Higuchi, Y.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 generated by PISA,PQS (software)

Macromolecule Content 

• Total Structure Weight: 42.84 kDa 
• Atom Count: 3,327 
• Modeled Residue Count: 378 
• Deposited Residue Count: 392 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
6-aminohexanoate-dimer hydrolase	A	392	Flavobacterium sp.	Mutation(s): 0  EC: 3.5.1.46
UniProt
Find proteins for P07062 (Paenarthrobacter ureafaciens) Explore P07062  Go to UniProtKB:  P07062

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.203 (Depositor), 0.203 (DCC) 
• R-Value Work:  0.185 (Depositor), 0.185 (DCC) 
• R-Value Observed: 0.185 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.37	α = 90
b = 96.37	β = 90
c = 113.09	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
MOSFLM	data reduction
CCP4	data scaling
SHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-09-20 
Deposition Author(s): Negoro, S., Ohki, T., Shibata, N., Mizuno, N., Wakitani, Y., Tsurukame, J., Matsumoto, K., Kawamoto, I., Takeo, M., Higuchi, Y.

Revision History  

• Version 1.0: 2005-09-20
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2017-08-23
  Changes: Source and taxonomy
• Version 1.4: 2024-03-13
  Changes: Data collection, Database references