7K1R | pdb_00007k1r

X-ray Structure of an Enterobacter GH43 Beta-Xylosidase: EcXyl43 F507A mutant

• PDB DOI: https://doi.org/10.2210/pdb7K1R/pdb

• Classification: HYDROLASE
• Organism(s): Enterobacter sp. enrichment culture clone nf1B6
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2020-09-08 Released: 2021-11-10 
• Deposition Author(s): Briganti, L., Capetti, C.C.M., Polikarpov, I.
• 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: 2.40 Å
• R-Value Free: 
  0.228 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.192 (Depositor) 

Starting Model: experimental

Literature

X-ray Structure of an Enterobacter GH43 Beta-Xylosidase: EcXyl43 F507A mutant

Briganti, L., Capetti, C.C.M., Polikarpov, I.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 244.04 kDa 
• Atom Count: 18,520 
• Modeled Residue Count: 2,133 
• Deposited Residue Count: 2,144 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta xylosidase GH43	A, B, C, D	536	Enterobacter sp. enrichment culture clone nf1B6	Mutation(s): 1  EC: 3.2.1.37
UniProt
Find proteins for V5J3M5 (Enterobacter sp. enrichment culture clone nf1B6) Explore V5J3M5  Go to UniProtKB:  V5J3M5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	F [auth B], I [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA	E [auth A], G [auth B], H [auth C], J [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.228 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.192 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.123	α = 90
b = 153.1	β = 90
c = 182.401	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-11-10 
Deposition Author(s): Briganti, L., Capetti, C.C.M., Polikarpov, I.

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Funding Organization	Location	Grant Number
Sao Paulo Research Foundation (FAPESP)	Brazil	2015/13684-0
Brazilian National Council for Scientific and Technological Development (CNPq)	Brazil	423693/2016-6
Brazilian National Council for Scientific and Technological Development (CNPq)	Brazil	303988/2016-9

Revision History  

• Version 1.0: 2021-11-10
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Refinement description