8WAC | pdb_00008wac

Crystal structure of a novel agarose-binding carbohydrate binding module of an agarase

PDB DOI: https://doi.org/10.2210/pdb8WAC/pdb

Classification: SUGAR BINDING PROTEIN
Organism(s): Wenyingzhuangia fucanilytica
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2023-09-07 Released: 2024-09-11
Deposition Author(s): Mei, X.W., Chang, Y.G.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free:
0.205 (Depositor), 0.202 (DCC)
R-Value Work:
0.168 (Depositor), 0.167 (DCC)
R-Value Observed:
0.172 (Depositor)

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

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

Literature

Crystal structure of a novel agarose-binding carbohydrate binding module of an agarase

Mei, X.W., Chang, Y.G.

To be published.

Macromolecule Content

Total Structure Weight: 14.28 kDa
Atom Count: 1,239
Modeled Residue Count: 119
Deposited Residue Count: 127
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Agarase	A	127	Wenyingzhuangia fucanilytica	Mutation(s): 0 Gene Names: AXE80_01580
UniProt
Find proteins for A0A1B1Y2R0 (Wenyingzhuangia fucanilytica) Explore A0A1B1Y2R0 Go to UniProtKB: A0A1B1Y2R0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A1B1Y2R0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CA Query on CA 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]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.205 (Depositor), 0.202 (DCC)
R-Value Work: 0.168 (Depositor), 0.167 (DCC)
R-Value Observed: 0.172 (Depositor)

Space Group: P 2₁ 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.661	α = 90
b = 48.651	β = 90
c = 67.314	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-09-11

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	U22A20542

Revision History (Full details and data files)

Version 1.0: 2024-09-11
Type: Initial release
Version 1.1: 2024-09-25
Changes: Derived calculations

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.