9VTV | pdb_00009vtv

Chitinase TfeC from Yersinia pseudotuberculosis

PDB DOI: https://doi.org/10.2210/pdb9VTV/pdb

Classification: HYDROLASE
Organism(s): Yersinia pseudotuberculosis YPIII
Expression System: Escherichia
Mutation(s): No

Deposited: 2025-07-11 Released: 2025-11-05
Deposition Author(s): Zhu, L.F., Zuo, Y.X., Cui, R., Li, D.F., Liu, S.J., Shen, X.H.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.208 (Depositor), 0.203 (DCC)
R-Value Work:
0.184 (Depositor), 0.180 (DCC)
R-Value Observed:
0.193 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment

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

Literature

Interkingdom Tyrosol Recognition Activates Antifungal Chitinase Secretion via T6SS

Zhu, L.F., Zuo, Y.X., Cui, R., Li, D.F., Liu, S.J., Shen, X.H.

To be published.

Macromolecule Content

Total Structure Weight: 60.14 kDa
Atom Count: 3,838
Modeled Residue Count: 420
Deposited Residue Count: 524
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DUF3142 domain-containing protein	A, B	262	Yersinia pseudotuberculosis YPIII	Mutation(s): 0 Gene Names: YPK_0957
UniProt
Find proteins for A0A0H3B0R1 (Yersinia pseudotuberculosis serotype O:3 (strain YPIII)) Explore A0A0H3B0R1 Go to UniProtKB: A0A0H3B0R1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0H3B0R1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SRT Query on SRT Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	S,R MESO-TARTARIC ACID C₄ H₆ O₆ FEWJPZIEWOKRBE-XIXRPRMCSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.208 (Depositor), 0.203 (DCC)
R-Value Work: 0.184 (Depositor), 0.180 (DCC)
R-Value Observed: 0.193 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.913	α = 90
b = 63.926	β = 90.18
c = 77.947	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
PHASER	phasing
XDS	data reduction

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-11-05

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	92051101

Revision History (Full details and data files)

Version 1.0: 2025-11-05
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.