7WOL | pdb_00007wol

Crystal structure of lipase TrLipB from Thermomocrobium roseum

PDB DOI: https://doi.org/10.2210/pdb7WOL/pdb

Classification: HYDROLASE
Organism(s): Thermomicrobium roseum DSM 5159
Expression System: Bacillus subtilis
Mutation(s): No

Deposited: 2022-01-21 Released: 2023-01-25
Deposition Author(s): Zhang, L., Fang, Y., Shi, Y., Gu, Z., Xin, Y.
Funding Organization(s): National Key Research and Development Program of China

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.186 (Depositor), 0.198 (DCC)
R-Value Work:
0.157 (Depositor), 0.170 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7WOL

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

Literature

Crystal structure of lipase TrLipB from Thermomocrobium roseum

Fang, Y., Xin, Y., Shi, Y., Gu, Z., Zhang, L.

To be published.

Macromolecule Content

Total Structure Weight: 75.07 kDa
Atom Count: 5,499
Modeled Residue Count: 638
Deposited Residue Count: 666
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lipase	A, B	333	Thermomicrobium roseum DSM 5159	Mutation(s): 0 Gene Names: trd_1687
UniProt
Find proteins for B9L0X7 (Thermomicrobium roseum (strain ATCC 27502 / DSM 5159 / P-2)) Explore B9L0X7 Go to UniProtKB: B9L0X7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B9L0X7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SIN Query on SIN Download:Ideal Coordinates CCD File SDF format, chain N [auth B] SDF format, chain C [auth A] MOL2 format, chain N [auth B] MOL2 format, chain C [auth A] mmCIF format, chain N [auth B] mmCIF format, chain C [auth A]	C [auth A], N [auth B]	SUCCINIC ACID C₄ H₆ O₄ KDYFGRWQOYBRFD-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain N [auth B] Interactions & Density Focus chain C [auth A] Focus chain N [auth B]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain Q [auth B] SDF format, chain O [auth B] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain O [auth B] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain O [auth B] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A], F [auth A], O [auth B], Q [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain O [auth B] Focus chain Q [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain O [auth B] Focus chain Q [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain U [auth B] SDF format, chain J [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain D [auth A] MOL2 format, chain U [auth B] MOL2 format, chain J [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain D [auth A] mmCIF format, chain U [auth B] mmCIF format, chain J [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain D [auth A]	D [auth A], G [auth A], H [auth A], J [auth A], U [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth A] Focus chain U [auth B] Interactions & Density Focus chain D [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth A] Focus chain U [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain V [auth B] SDF format, chain T [auth B] SDF format, chain S [auth B] SDF format, chain R [auth B] SDF format, chain P [auth B] SDF format, chain M [auth A] SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain I [auth A] MOL2 format, chain V [auth B] MOL2 format, chain T [auth B] MOL2 format, chain S [auth B] MOL2 format, chain R [auth B] MOL2 format, chain P [auth B] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain I [auth A] mmCIF format, chain V [auth B] mmCIF format, chain T [auth B] mmCIF format, chain S [auth B] mmCIF format, chain R [auth B] mmCIF format, chain P [auth B] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain I [auth A]	I [auth A] K [auth A] L [auth A] M [auth A] P [auth B] I [auth A], K [auth A], L [auth A], M [auth A], P [auth B], R [auth B], S [auth B], T [auth B], V [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain P [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain V [auth B] Interactions & Density Focus chain I [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain P [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain V [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.186 (Depositor), 0.198 (DCC)
R-Value Work: 0.157 (Depositor), 0.170 (DCC)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 129.402	α = 90
b = 129.402	β = 90
c = 122.792	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2023-01-25

Deposition Author(s):

Funding Organization	Location	Grant Number
National Key Research and Development Program of China	China	2018YFA0900300
National Key Research and Development Program of China	China	2021YFC2100300

Revision History (Full details and data files)

Version 1.0: 2023-01-25
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, 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.