8Y6T | pdb_00008y6t

Chitinase TfeC from Yersinia pseudotuberculosis

PDB DOI: https://doi.org/10.2210/pdb8Y6T/pdb

Classification: HYDROLASE
Organism(s): Yersinia pseudotuberculosis B-6862
Expression System: Escherichia
Mutation(s): No

Deposited: 2024-02-03 Released: 2025-02-05
Deposition Author(s): Cui, R., Li, D.F.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.288 (Depositor), 0.289 (DCC)
R-Value Work:
0.241 (Depositor), 0.243 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8Y6T

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

Literature

Structure of chitinase at 1.9 Angstroms resolution.

Cui, R., Li, D.F.

To be published.

Macromolecule Content

Total Structure Weight: 120.28 kDa
Atom Count: 7,763
Modeled Residue Count: 843
Deposited Residue Count: 1,048
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DUF3142 domain-containing protein	A, B, C, D	262	Yersinia pseudotuberculosis B-6862	Mutation(s): 0 Gene Names: EGX52_02760
UniProt
Find proteins for A0A0U1R086 (Yersinia pseudotuberculosis serotype O:1b (strain IP 31758)) Explore A0A0U1R086 Go to UniProtKB: A0A0U1R086
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0U1R086
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TLA Query on TLA Download:Ideal Coordinates CCD File SDF format, chain H [auth D] SDF format, chain G [auth C] SDF format, chain F [auth B] SDF format, chain E [auth A] MOL2 format, chain H [auth D] MOL2 format, chain G [auth C] MOL2 format, chain F [auth B] MOL2 format, chain E [auth A] mmCIF format, chain H [auth D] mmCIF format, chain G [auth C] mmCIF format, chain F [auth B] mmCIF format, chain E [auth A]	E [auth A], F [auth B], G [auth C], H [auth D]	L(+)-TARTARIC ACID C₄ H₆ O₆ FEWJPZIEWOKRBE-JCYAYHJZSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D	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: 0.288 (Depositor), 0.289 (DCC)
R-Value Work: 0.241 (Depositor), 0.243 (DCC)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.891	α = 90
b = 63.849	β = 90
c = 77.854	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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Entry History

& Funding Information

Deposition Data

Released Date: 2025-02-05

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: 2025-02-05
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.