7YKP | pdb_00007ykp

Crystal structure of a novel alpha/beta hydrolase from thermomonospora curvata with glycerol

PDB DOI: https://doi.org/10.2210/pdb7YKP/pdb

Classification: HYDROLASE
Organism(s): Thermomonospora curvata DSM 43183
Expression System: Trichoderma reesei QM6a
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: 1.18 Å
R-Value Free:
0.168 (Depositor), 0.175 (DCC)
R-Value Work:
0.158 (Depositor), 0.168 (DCC)
R-Value Observed:
0.158 (Depositor)

Starting Model: experimental
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This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of a novel alpha/beta hydrolase from thermomonospora curvata with glycerol

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

To be published.

Macromolecule Content

Total Structure Weight: 28.51 kDa
Atom Count: 2,448
Modeled Residue Count: 260
Deposited Residue Count: 260
Unique protein chains: 1

Macromolecules

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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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	D1A9G5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL 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]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-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: 1.18 Å
R-Value Free: 0.168 (Depositor), 0.175 (DCC)
R-Value Work: 0.158 (Depositor), 0.168 (DCC)
R-Value Observed: 0.158 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.63	α = 90
b = 71.58	β = 90
c = 143.21	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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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: 2024-11-06
Changes: Data collection, Structure summary
Version 1.2: 2026-03-04
Changes: Refinement description

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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.