6X2Q | pdb_00006x2q

Complex of Gynuella sunshinyii GH46 chitosanase GsCsn46A with chitotetraose

PDB DOI: https://doi.org/10.2210/pdb6X2Q/pdb

Classification: SUGAR BINDING PROTEIN
Organism(s): Gynuella sunshinyii YC6258
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2020-05-20 Released: 2021-05-26
Deposition Author(s): Qin, Z., Wang, Y.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.27 Å
R-Value Free:
0.228 (Depositor)
R-Value Work:
0.185 (Depositor), 0.191 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Complex of Gynuella sunshinyii GH46 chitosanase GsCsn46A with chitotetraose

Qin, Z., Wang, Y.

To be published.

Macromolecule Content

Total Structure Weight: 27.74 kDa
Atom Count: 1,975
Modeled Residue Count: 242
Deposited Residue Count: 243
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chitosanase	A	243	Gynuella sunshinyii YC6258	Mutation(s): 0 Gene Names: YC6258_05941
UniProt
Find proteins for A0A0C5VFC0 (Gynuella sunshinyii YC6258) Explore A0A0C5VFC0 Go to UniProtKB: A0A0C5VFC0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0C5VFC0
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-amino-2-deoxy-beta-D-glucopyranose-(1-4)-2-amino-2-deoxy-beta-D-glucopyranose-(1-4)-2-amino-2-deoxy-beta-D-glucopyranose	B	3		N/A	Interactions Focus chain B Interactions & Density Focus chain B
Glycosylation Resources
GlyTouCan: G36121RO GlyCosmos: G36121RO

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GCS (Subject of Investigation/LOI) Query on GCS 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]	2-amino-2-deoxy-beta-D-glucopyranose C₆ H₁₃ N O₅ MSWZFWKMSRAUBD-QZABAPFNSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.27 Å
R-Value Free: 0.228 (Depositor)
R-Value Work: 0.185 (Depositor), 0.191 (DCC)

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.756	α = 90
b = 83.756	β = 90
c = 117.31	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2021-05-26

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	31701537

Revision History (Full details and data files)

Version 1.0: 2021-05-26
Type: Initial release
Version 1.1: 2023-10-18
Changes: Data collection, Database references, Refinement description

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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.