7JVH

Crystal structure of a GH43_12 retrieved from capybara gut metagenome

• PDB DOI: https://doi.org/10.2210/pdb7JVH/pdb

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


• Deposited: 2020-08-21 Released: 2021-09-08 
• Deposition Author(s): Cabral, L., Domingues, M.N., Martins, M.P., Persinoti, G.F., Morais, M.A.B., Murakami, M.T.
• Funding Organization(s): Sao Paulo Research Foundation (FAPESP), Brazilian National Council for Scientific and Technological Development (CNPq)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.48 Å
• R-Value Free: 0.278 
• R-Value Work: 0.246 
• R-Value Observed: 0.248 

Literature

Crystal structure of a GH43_12 retrieved from capybara gut metagenome

Cabral, L., Domingues, M.N., Martins, M.P., Persinoti, G.F., Morais, M.A.B., Murakami, M.T.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 assigned by authors and generated by PISA (software)

Biological Assembly 5  

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

Biological assembly 5 assigned by authors and generated by PISA (software)

Biological Assembly 6  

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

Biological assembly 6 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 384.65 kDa 
• Atom Count: 25,078 
• Modelled Residue Count: 3,136 
• Deposited Residue Count: 3,402 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycoside Hydrolase Family 43_12	A, B, C, D, E, F	567	metagenome	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	G [auth A], H [auth A], I [auth A], J [auth B], K [auth B], L [auth C], M [auth C], N [auth D], O [auth D], P [auth F]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.48 Å
• R-Value Free: 0.278 
• R-Value Work: 0.246 
• R-Value Observed: 0.248 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.223	α = 99.03
b = 107.383	β = 113.38
c = 132.533	γ = 108.45

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-09-08 
Deposition Author(s): Cabral, L., Domingues, M.N., Martins, M.P., Persinoti, G.F., Morais, M.A.B., Murakami, M.T.

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Funding Organization	Location	Grant Number
Sao Paulo Research Foundation (FAPESP)	Brazil	2015/26982-0
Brazilian National Council for Scientific and Technological Development (CNPq)	Brazil	306135/2016-7
Brazilian National Council for Scientific and Technological Development (CNPq)	Brazil	408600/2018-7
Brazilian National Council for Scientific and Technological Development (CNPq)	Brazil	439195/2016-02018-7
Brazilian National Council for Scientific and Technological Development (CNPq)	Brazil	142332/2017-8

Revision History  

• Version 1.0: 2021-09-08
  Type: Initial release