7ZYC | pdb_00007zyc

BeKdgF with Zn

• PDB DOI: https://doi.org/10.2210/pdb7ZYC/pdb

• Classification: HYDROLASE
• Organism(s): Bacteroides eggerthii DSM 20697
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2022-05-24 Released: 2023-06-14 
• Deposition Author(s): Fredslund, F., Teze, D., Welner, D.H.
• Funding Organization(s): Novo Nordisk Foundation, Danish Agency for Science Technology and Innovation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.260 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.228 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.231 (Depositor) 

Starting Model: experimental

Literature

BeKdgF with Ca

Fredslund, F., Teze, D., Welner, D.H.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 15.22 kDa 
• Atom Count: 888 
• Modeled Residue Count: 111 
• Deposited Residue Count: 134 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cupin	A	134	Bacteroides eggerthii DSM 20697	Mutation(s): 0  Gene Names: DW701_08695, DWZ51_01720, EAJ03_07795, NCTC11155_02558
UniProt
Find proteins for A0A380Z821 (Bacteroides eggerthii) Explore A0A380Z821  Go to UniProtKB:  A0A380Z821

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	B [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	C [auth A], D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.260 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.228 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.231 (Depositor) 

Space Group: P 6₂ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.66	α = 90
b = 46.66	β = 90
c = 176.96	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-06-14 
Deposition Author(s): Fredslund, F., Teze, D., Welner, D.H.

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Funding Organization	Location	Grant Number
Novo Nordisk Foundation	Denmark	NNF20CC0035580
Danish Agency for Science Technology and Innovation	Denmark	7129-00003B

Revision History  

• Version 1.0: 2023-06-14
  Type: Initial release
  
• Version 1.1: 2024-02-07
  Changes: Data collection, Refinement description