9KB3 | pdb_00009kb3

The structure of the carbohydrate deacetylase inactive mutant PpOngB in complex with GlcNAc1A.

PDB DOI: https://doi.org/10.2210/pdb9KB3/pdb

Classification: PROTEIN BINDING
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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.29 Å
R-Value Free:
0.219 (Depositor), 0.219 (DCC)
R-Value Work:
0.173 (Depositor), 0.173 (DCC)
R-Value Observed:
0.176 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Structure of the PpOngB-GlcNAc1A

Wang, J.P.

To be published.

Macromolecule Content

Total Structure Weight: 53.33 kDa
Atom Count: 3,953
Modeled Residue Count: 478
Deposited Residue Count: 489
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carbohydrate de-N-acetylated protein	A	489	Pseudoalteromonas prydzensis ACAM 620	Mutation(s): 0
UniProt
Find proteins for A0A7V1CY72 (Pseudoalteromonas prydzensis) Explore A0A7V1CY72 Go to UniProtKB: A0A7V1CY72
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A7V1CY72
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1EEZ Query on A1EEZ Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	(2~{R},3~{R},4~{S},5~{R})-2-acetamido-3,4,5,6-tetrakis(oxidanyl)hexanoic acid C₈ H₁₅ N O₇ LZKNVSNNPRQZJB-LMMQKCLSSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.29 Å
R-Value Free: 0.219 (Depositor), 0.219 (DCC)
R-Value Work: 0.173 (Depositor), 0.173 (DCC)
R-Value Observed: 0.176 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.818	α = 90
b = 86.818	β = 90
c = 141.644	γ = 120

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-03-19

Deposition Author(s):

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

Revision History (Full details and data files)

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.