9KB4 | pdb_00009kb4

The structure of the PpOngB-citrate

PDB DOI: https://doi.org/10.2210/pdb9KB4/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: 2025-10-08
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: 1.85 Å
R-Value Free:
0.191 (Depositor), 0.192 (DCC)
R-Value Work:
0.164 (Depositor), 0.165 (DCC)
R-Value Observed:
0.166 (Depositor)

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

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

Literature

Structure of the complexes of PpOngB binding with citrate

Wang, J.P., Wang, J.P.

To be published.

Macromolecule Content

Total Structure Weight: 53.29 kDa
Atom Count: 4,229
Modeled Residue Count: 480
Deposited Residue Count: 489
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CIT Query on CIT 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]	CITRIC ACID C₆ H₈ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
ZN (Subject of Investigation/LOI) 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: 1.85 Å
R-Value Free: 0.191 (Depositor), 0.192 (DCC)
R-Value Work: 0.164 (Depositor), 0.165 (DCC)
R-Value Observed: 0.166 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.286	α = 90
b = 88.286	β = 90
c = 143.524	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
HKL-3000	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-10-08

Deposition Author(s):

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

Revision History (Full details and data files)

Version 1.0: 2025-10-08
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.