3A66

Crystal structure of 6-aminohexanoate-dimer hydrolase S112A/G181D/H266N/D370Y mutant with substrate

PDB DOI: https://doi.org/10.2210/pdb3A66/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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.225
R-Value Work: 0.210
R-Value Observed: 0.210

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 2.0 of the entry. See complete history.

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.

Macromolecule Content

Total Structure Weight: 44.12 kDa
Atom Count: 3,394
Modelled Residue Count: 378
Deposited Residue Count: 392
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
6-AMINOHEXANOATE-DIMER HYDROLASE	A	392	Paenarthrobacter ureafaciens	Mutation(s): 4 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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Groups	P07061P07062
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MES Query on MES Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A]	K [auth A], L [auth A]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain L [auth A] Interactions & Density Focus chain K [auth A] Focus chain L [auth A]
ACA Query on ACA Download Ideal Coordinates CCD File SDF format, chain M [auth A] MOL2 format, chain M [auth A] mmCIF format, chain M [auth A]	M [auth A]	6-AMINOHEXANOIC ACID C₆ H₁₃ N O₂ SLXKOJJOQWFEFD-UHFFFAOYSA-N		Interactions Focus chain M [auth A] Interactions & Density Focus chain M [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain H [auth A] SDF format, chain J [auth A] SDF format, chain G [auth A] SDF format, chain I [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth A] MOL2 format, chain J [auth A] MOL2 format, chain G [auth A] MOL2 format, chain I [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain H [auth A] mmCIF format, chain J [auth A] mmCIF format, chain G [auth A] mmCIF format, chain I [auth A]	D [auth A] E [auth A] F [auth A] G [auth A] H [auth A] D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A]	B [auth A], C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.225
R-Value Work: 0.210
R-Value Observed: 0.210
Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.524	α = 90
b = 96.524	β = 90
c = 113.089	γ = 120

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2010-09-01

Deposition Author(s):

Revision History (Full details and data files)

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: Advisory, Refinement description, Source and taxonomy
Version 1.3: 2023-11-01
Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description
Version 2.0: 2023-11-15
Changes: Atomic model, Data collection

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Help and Resources

3A66

Crystal structure of 6-aminohexanoate-dimer hydrolase S112A/G181D/H266N/D370Y mutant with substrate

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

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)