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), 0.172 (DCC)
R-Value Observed:
0.176 (Depositor)

Starting Model: in silico
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Ligand Structure Quality Assessment

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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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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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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), 0.172 (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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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

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.