9KB1 | pdb_00009kb1

The Structure of the Carbohydrate Deacetylase PpOngB from Pseudoalteromonas prydzensis ACAM 620.

• PDB DOI: https://doi.org/10.2210/pdb9KB1/pdb

• Classification: DE NOVO PROTEIN
• Organism(s): Pseudoalteromonas prydzensis ACAM 620
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-10-30 Released: 2025-03-19 
• Deposition Author(s): Wang, J.P., Li, P.Y.
• Funding Organization(s): National Science Foundation (NSF, China)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free: 
  0.199 (Depositor), 0.199 (DCC) 
• R-Value Work: 
  0.172 (Depositor), 0.172 (DCC) 

Starting Model: in silico

Literature

Structure of the wild-type PpOngB

Wang, J.P.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 53.24 kDa 
• Atom Count: 4,131 
• Modeled Residue Count: 476 
• Deposited Residue Count: 489 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PpOngB	A	489	Pseudoalteromonas prydzensis ACAM 620	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free:  0.199 (Depositor), 0.199 (DCC) 
• R-Value Work:  0.172 (Depositor), 0.172 (DCC) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.597	α = 90
b = 87.597	β = 90
c = 143.319	γ = 120

Software Package:

Software Name	Purpose
HKL-3000	data collection
PDB_EXTRACT	data extraction
autoPROC	data processing
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-03-19 
Deposition Author(s): Wang, J.P., Li, P.Y.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, China)	China	--

Revision History  

• Version 1.0: 2025-03-19
  Type: Initial release