3VWP

Crystal structure of 6-aminohexanoate-dimer hydrolase S112A/G181D/R187S/H266N/D370Y mutant complexd with 6-aminohexanoate

PDB DOI: https://doi.org/10.2210/pdb3VWP/pdb

Classification: HYDROLASE
Organism(s): Paenarthrobacter ureafaciens, Flavobacterium sp. KI723T1
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2012-08-30 Released: 2013-10-16
Deposition Author(s): Kawashima, Y., Shibata, N., Negoro, S., Higuchi, Y.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free: 0.219
R-Value Work: 0.198

wwPDB Validation 3D Report Full Report

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

Literature

Structural, kinetic and theoretical analyses of hydrolase mutants altering in the directionality and equilibrium point of reversible amide-synthetic/hydrolytic reaction

Negoro, S., Kawashima, Y., Shibata, N., Shigeta, Y., Kobayashi, T., Nishiguchi, H., Matsui, T., Baba, T., Lee, Y., Kamiya, K., Kato, D., Takeo, M., Higuchi, Y.

To be published.

Macromolecule Content

Total Structure Weight: 43.84 kDa
Atom Count: 3,489
Modelled Residue Count: 384
Deposited Residue Count: 392
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
6-aminohexanoate-dimer hydrolase	A	392	Paenarthrobacter ureafaciens, Flavobacterium sp. KI723T1 This entity is chimeric	Mutation(s): 5 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 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MES Query on MES Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A]	I [auth A], J [auth A]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Interactions & Density Focus chain I [auth A] Focus chain J [auth A]
ACA Query on ACA Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	6-AMINOHEXANOIC ACID C₆ H₁₃ N O₂ SLXKOJJOQWFEFD-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A]	E [auth A], F [auth A], G [auth A], H [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free: 0.219
R-Value Work: 0.198
Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.39	α = 90
b = 96.39	β = 90
c = 112.87	γ = 120

Software Package:

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

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2013-10-16

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-10-16
Type: Initial release
Version 2.0: 2023-11-15
Changes: Atomic model, Data collection, Database references, Derived calculations

Prepare Data

Validate Data

Deposit Data

Help and Resources

3VWP

Crystal structure of 6-aminohexanoate-dimer hydrolase S112A/G181D/R187S/H266N/D370Y mutant complexd with 6-aminohexanoate

Structural, kinetic and theoretical analyses of hydrolase mutants altering in the directionality and equilibrium point of reversible amide-synthetic/hydrolytic reaction

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)