8WZY | pdb_00008wzy

A novel amidohydrolase

• PDB DOI: https://doi.org/10.2210/pdb8WZY/pdb

• Classification: HYDROLASE
• Organism(s): Klebsiella sp. PCX
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-11-02 Released: 2024-11-13 
• Deposition Author(s): Feng, R., Ma, D.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.87 Å
• R-Value Free: 
  0.260 (Depositor), 0.266 (DCC) 
• R-Value Work: 
  0.212 (Depositor), 0.224 (DCC) 
• R-Value Observed: 
  0.214 (Depositor) 

Starting Model: in silico

Literature

A novel amidohydrolase catalyzes the degradation of polyacrylamide by Klebsiella sp. PCX

Ma, D., Feng, R.

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)

Macromolecule Content 

• Total Structure Weight: 41.26 kDa 
• Atom Count: 2,907 
• Modeled Residue Count: 376 
• Deposited Residue Count: 377 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydroorotase	A	377	Klebsiella sp. PCX	Mutation(s): 0  Gene Names: A9P88_23745

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	F [auth A], G [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	B [auth A], C [auth A], D [auth A], E [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
KCX	A	L-PEPTIDE LINKING	C7 H14 N2 O4		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.87 Å
• R-Value Free:  0.260 (Depositor), 0.266 (DCC) 
• R-Value Work:  0.212 (Depositor), 0.224 (DCC) 
• R-Value Observed: 0.214 (Depositor) 

Space Group: P 2₁ 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 179.745	α = 90
b = 42.002	β = 90
c = 43.557	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-11-13 
Deposition Author(s): Feng, R., Ma, D.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32101371

Revision History  

• Version 1.0: 2024-11-13
  Type: Initial release