3VWN | pdb_00003vwn

Crystal structure of 6-aminohexanoate-dimer hydrolase G181D/R187G/H266N/D370Y mutant

PDB DOI: https://doi.org/10.2210/pdb3VWN/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: 1.20 Å
R-Value Free:
0.146 (Depositor), 0.153 (DCC)
R-Value Work:
0.130 (Depositor), 0.139 (DCC)
R-Value Observed:
0.130 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3VWN

This is version 1.1 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: 44.22 kDa
Atom Count: 3,560
Modeled Residue Count: 384
Deposited Residue Count: 392
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
6-aminohexanoate-dimer hydrolase	A [auth X]	392	Paenarthrobacter ureafaciens, Flavobacterium sp. KI723T1 This entity is chimeric	Mutation(s): 4 Gene Names: nylB, nylB' EC: 3.5.1.46
UniProt
Find proteins for P07061 (Paenarthrobacter ureafaciens) Explore P07061 Go to UniProtKB: P07061
Find proteins for P07062 (Paenarthrobacter ureafaciens) Explore P07062 Go to UniProtKB: P07062
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Groups	P07061 P07062
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 I [auth X] SDF format, chain H [auth X] SDF format, chain G [auth X] MOL2 format, chain I [auth X] MOL2 format, chain H [auth X] MOL2 format, chain G [auth X] mmCIF format, chain I [auth X] mmCIF format, chain H [auth X] mmCIF format, chain G [auth X]	G [auth X], H [auth X], I [auth X]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain G [auth X] Focus chain H [auth X] Focus chain I [auth X] Interactions & Density Focus chain G [auth X] Focus chain H [auth X] Focus chain I [auth X]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain L [auth X] SDF format, chain K [auth X] SDF format, chain J [auth X] MOL2 format, chain L [auth X] MOL2 format, chain K [auth X] MOL2 format, chain J [auth X] mmCIF format, chain L [auth X] mmCIF format, chain K [auth X] mmCIF format, chain J [auth X]	J [auth X], K [auth X], L [auth X]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain J [auth X] Focus chain K [auth X] Focus chain L [auth X] Interactions & Density Focus chain J [auth X] Focus chain K [auth X] Focus chain L [auth X]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain F [auth X] SDF format, chain E [auth X] SDF format, chain D [auth X] SDF format, chain C [auth X] SDF format, chain B [auth X] MOL2 format, chain F [auth X] MOL2 format, chain E [auth X] MOL2 format, chain D [auth X] MOL2 format, chain C [auth X] MOL2 format, chain B [auth X] mmCIF format, chain F [auth X] mmCIF format, chain E [auth X] mmCIF format, chain D [auth X] mmCIF format, chain C [auth X] mmCIF format, chain B [auth X]	B [auth X], C [auth X], D [auth X], E [auth X], F [auth X]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain B [auth X] Focus chain C [auth X] Focus chain D [auth X] Focus chain E [auth X] Focus chain F [auth X] Interactions & Density Focus chain B [auth X] Focus chain C [auth X] Focus chain D [auth X] Focus chain E [auth X] Focus chain F [auth X]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain O [auth X] SDF format, chain N [auth X] SDF format, chain M [auth X] MOL2 format, chain O [auth X] MOL2 format, chain N [auth X] MOL2 format, chain M [auth X] mmCIF format, chain O [auth X] mmCIF format, chain N [auth X] mmCIF format, chain M [auth X]	M [auth X], N [auth X], O [auth X]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain M [auth X] Focus chain N [auth X] Focus chain O [auth X] Interactions & Density Focus chain M [auth X] Focus chain N [auth X] Focus chain O [auth X]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.20 Å
R-Value Free: 0.146 (Depositor), 0.153 (DCC)
R-Value Work: 0.130 (Depositor), 0.139 (DCC)
R-Value Observed: 0.130 (Depositor)

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.64	α = 90
b = 96.64	β = 90
c = 112.996	γ = 120

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction

Structure Validation

View Full Validation Report

View more in-depth experimental data

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 1.1: 2024-03-20
Changes: Data collection, Database references, Derived calculations

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.