6NKG | pdb_00006nkg

Crystal Structure of the Lipase Lip_vut5 from Goat Rumen metagenome.

PDB DOI: https://doi.org/10.2210/pdb6NKG/pdb

Classification: HYDROLASE
Organism(s): metagenome
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2019-01-07 Released: 2020-01-22
Deposition Author(s): Kim, Y., Welk, L., Mukendi, G., Nkhi, G., Motloi, T., Jedrzejczak, R., Feto, N., Joachimiak, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free:
0.235 (Depositor), 0.245 (DCC)
R-Value Work:
0.195 (Depositor), 0.206 (DCC)
R-Value Observed:
0.197 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal Structure of the Lipase Lip_vut5 from Goat Rumen metagenome.

Kim, Y., Welk, L., Jedrzejczak, R., Feto, N., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 29.93 kDa
Atom Count: 2,102
Modeled Residue Count: 245
Deposited Residue Count: 254
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lip_vut5, C4L	A	254	metagenome	Mutation(s): 0 EC: 3.1.1.1
UniProt
Find proteins for Q65EQ1 (Bacillus licheniformis (strain ATCC 14580 / DSM 13 / JCM 2505 / CCUG 7422 / NBRC 12200 / NCIMB 9375 / NCTC 10341 / NRRL NRS-1264 / Gibson 46)) Explore Q65EQ1 Go to UniProtKB: Q65EQ1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q65EQ1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO 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]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-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]
ACY Query on ACY 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]	ACETIC ACID C₂ H₄ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.235 (Depositor), 0.245 (DCC)
R-Value Work: 0.195 (Depositor), 0.206 (DCC)
R-Value Observed: 0.197 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.11	α = 90
b = 60.11	β = 90
c = 169.898	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
MLPHARE	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2020-01-22

Deposition Author(s):

Jedrzejczak, R.

Revision History (Full details and data files)

Version 1.0: 2020-01-22
Type: Initial release
Version 1.1: 2024-10-16
Changes: Data collection, Database references, Structure summary

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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.