7YKO | pdb_00007yko

Crystal structure of a novel alpha/beta hydrolase mutant from thermomonospora curvata in complex with pentane-1,5-diol

PDB DOI: https://doi.org/10.2210/pdb7YKO/pdb

Classification: HYDROLASE
Organism(s): Thermomonospora curvata DSM 43183
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2022-07-23 Released: 2023-07-26
Deposition Author(s): Han, X., Jian, G., Bornscheuer, U.T., Wei, R., Liu, W.
Funding Organization(s): Chinese Scholarship Council, Chinese Academy of Sciences

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.15 Å
R-Value Free:
0.180 (Depositor), 0.180 (DCC)
R-Value Work:
0.169 (Depositor), 0.170 (DCC)
R-Value Observed:
0.170 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of a novel alpha/beta hydrolase mutant from thermomonospora curvata in complex with pentane-1,5-diol

Han, X., Jian, G., Bornscheuer, U.T., Wei, R., Liu, W.

To be published.

Macromolecule Content

Total Structure Weight: 28.62 kDa
Atom Count: 2,436
Modeled Residue Count: 259
Deposited Residue Count: 260
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Triacylglycerol lipase	A	260	Thermomonospora curvata DSM 43183	Mutation(s): 0 Gene Names: Tcur_1278 EC: 3.1.1.3 (PDB Primary Data), 3.1.1.101 (UniProt), 3.1.1.74 (UniProt)
UniProt
Find proteins for D1A9G5 (Thermomonospora curvata (strain ATCC 19995 / DSM 43183 / JCM 3096 / KCTC 9072 / NBRC 15933 / NCIMB 10081 / Henssen B9)) Explore D1A9G5 Go to UniProtKB: D1A9G5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	D1A9G5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
9JE (Subject of Investigation/LOI) Query on 9JE Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [auth A]	B [auth A], C [auth A]	pentane-1,5-diol C₅ H₁₂ O₂ ALQSHHUCVQOPAS-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: 1.15 Å
R-Value Free: 0.180 (Depositor), 0.180 (DCC)
R-Value Work: 0.169 (Depositor), 0.170 (DCC)
R-Value Observed: 0.170 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.66	α = 90
b = 71.6	β = 90
c = 143.22	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2023-07-26

Deposition Author(s):

Bornscheuer, U.T.

Funding Organization	Location	Grant Number
Chinese Scholarship Council	China	--
Chinese Academy of Sciences	China	--

Revision History (Full details and data files)

Version 1.0: 2023-07-26
Type: Initial release
Version 1.1: 2024-10-16
Changes: Data collection, Structure summary

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.