7SEV | pdb_00007sev

Crystal structure of E coli contaminant protein YadF co-purified with a plant protein

• PDB DOI: https://doi.org/10.2210/pdb7SEV/pdb

• Classification: LYASE
• Organism(s): Escherichia coli
• Mutation(s): No 


• Deposited: 2021-10-01 Released: 2021-11-03 
• Deposition Author(s): Chai, L., Zhu, P., Chai, J., Pang, C., Andi, B., McsWeeney, S., Shanklin, J., Liu, Q.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Department of Energy (DOE, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.243 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.204 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.206 (Depositor) 

Starting Model: in silico

Literature

AlphaFold Protein Structure Database for Sequence-Independent Molecular Replacement

Chai, L., Zhu, P., Chai, J., Pang, C., Andi, B., McSweeney, S., Shanklin, J., Liu, Q.

(2021) Crystals (Basel) 11

• DOI: https://doi.org/10.3390/cryst11101227

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: 25.24 kDa 
• Atom Count: 1,758 
• Modeled Residue Count: 211 
• Deposited Residue Count: 220 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carbonic anhydrase 2	A	220	Escherichia coli	Mutation(s): 0  EC: 4.2.1.1
UniProt
Find proteins for P61517 (Escherichia coli (strain K12)) Explore P61517  Go to UniProtKB:  P61517

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN (Subject of Investigation/LOI)	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
K	C [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.243 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.204 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.206 (Depositor) 

Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.5	α = 90
b = 67.5	β = 90
c = 85.212	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
DIALS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-11-03 
Deposition Author(s): Chai, L., Zhu, P., Chai, J., Pang, C., Andi, B., McsWeeney, S., Shanklin, J., Liu, Q.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	--
Department of Energy (DOE, United States)	United States	--

Revision History  

• Version 1.0: 2021-11-03
  Type: Initial release
  
• Version 1.1: 2022-04-20
  Changes: Database references
• Version 1.2: 2024-04-03
  Changes: Data collection, Refinement description