6NKC | pdb_00006nkc

Crystal Structure of the Lipase Lip_vut1 from Goat Rumen metagenome.

• PDB DOI: https://doi.org/10.2210/pdb6NKC/pdb

• Classification: HYDROLASE
• Organism(s): metagenome
• Expression System: Escherichia coli
• Mutation(s): No 
• Membrane Protein: Yes  OPM


• 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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.63 Å
• R-Value Free: 
  0.189 (Depositor), 0.189 (DCC) 
• R-Value Work: 
  0.157 (Depositor), 0.159 (DCC) 
• R-Value Observed: 
  0.159 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of the Lipase Lip_vut1 from Goat Rumen metagenome.

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

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 39.46 kDa 
• Atom Count: 2,982 
• Modeled Residue Count: 343 
• Deposited Residue Count: 362 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lipase, Lip_vut1	A, B	181	metagenome	Mutation(s): 0  EC: 3.1.1.3 Membrane Entity: Yes
UniProt
Find proteins for Q65HR4 (Bacillus licheniformis (strain ATCC 14580 / DSM 13 / JCM 2505 / CCUG 7422 / NBRC 12200 / NCIMB 9375 / NCTC 10341 / NRRL NRS-1264 / Gibson 46)) Explore Q65HR4  Go to UniProtKB:  Q65HR4

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	D [auth A], G [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
AZI	E [auth A]	AZIDE ION N3 IVRMZWNICZWHMI-UHFFFAOYSA-N
CL	C [auth A], F [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.63 Å
• R-Value Free:  0.189 (Depositor), 0.189 (DCC) 
• R-Value Work:  0.157 (Depositor), 0.159 (DCC) 
• R-Value Observed: 0.159 (Depositor) 

Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.87	α = 90
b = 49.87	β = 90
c = 141.625	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

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

Revision History  

• Version 1.0: 2020-01-22
  Type: Initial release
  
• Version 1.1: 2023-10-11
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2023-11-15
  Changes: Data collection
• Version 1.3: 2024-11-20
  Changes: Structure summary