3A65

Crystal structure of 6-aminohexanoate-dimer hydrolase S112A/G181D/H266N mutant with substrate

• PDB DOI: https://doi.org/10.2210/pdb3A65/pdb

• Classification: HYDROLASE
• Organism(s): Paenarthrobacter ureafaciens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2009-08-21 Released: 2010-09-01 
• Deposition Author(s): Kawashima, Y., Shibata, N., Higuchi, Y., Takeo, M., Negoro, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.201 
• R-Value Work: 0.180 
• R-Value Observed: 0.180 

Literature

Enzymatic Synthesis of Nylon-6 Units in Organic Sol Contained Low-Water: Structural Requirement of 6-Aminohexanoate-Dimer Hydrolase for Efficient Amid Synthesis

Kawashima, Y., Yasuhira, K., Shibata, N., Matsuura, Y., Tanaka, Y., Taniguchi, M., Miyoshi, Y., Takeo, M., Kato, D., Higuchi, Y., Negoro, S.

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 PISA (software)

Macromolecule Content

• Total Structure Weight: 43.68 kDa 
• Atom Count: 3,498 
• Modelled Residue Count: 384 
• 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	Paenarthrobacter ureafaciens	Mutation(s): 3  Gene Names: nylB, NYLB' EC: 3.5.1.46
UniProt
Find proteins for P07062 (Paenarthrobacter ureafaciens) Explore P07062  Go to UniProtKB:  P07062
Find proteins for P07061 (Paenarthrobacter ureafaciens) Explore P07061  Go to UniProtKB:  P07061
UniProt Groups	P07061P07062

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MES	C [auth A], D [auth A]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N
ACA	B [auth A]	6-AMINOHEXANOIC ACID C6 H13 N O2 SLXKOJJOQWFEFD-UHFFFAOYSA-N
GOL	E [auth A], F [auth A], G [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
NA	H [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.201 
• R-Value Work: 0.180 
• R-Value Observed: 0.180 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.414	α = 90
b = 96.414	β = 90
c = 112.869	γ = 120

Software Package:

Software Name	Purpose
CrystalClear	data collection
CNS	refinement
d*TREK	data reduction
d*TREK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-09-01 
Deposition Author(s): Kawashima, Y., Shibata, N., Higuchi, Y., Takeo, M., Negoro, S.

Revision History  

• Version 1.0: 2010-09-01
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-08-09
  Changes: Refinement description, Source and taxonomy
• Version 1.3: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection