8WAE | pdb_00008wae

Crystal structure of a novel porphyran-binding carbohydrate binding module

• PDB DOI: https://doi.org/10.2210/pdb8WAE/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Flammeovirga sp. OC4
• 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): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 
  0.207 (Depositor), 0.208 (DCC) 
• R-Value Work: 
  0.157 (Depositor), 0.158 (DCC) 
• R-Value Observed: 
  0.162 (Depositor) 

Starting Model: in silico

Literature

Crystal structure of a novel porphyran-binding carbohydrate binding module

Mei, X.W., Chang, Y.G.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 25.03 kDa 
• Atom Count: 2,094 
• Modeled Residue Count: 214 
• Deposited Residue Count: 236 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-agarase	A, B	118	Flammeovirga sp. OC4	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free:  0.207 (Depositor), 0.208 (DCC) 
• R-Value Work:  0.157 (Depositor), 0.158 (DCC) 
• R-Value Observed: 0.162 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 25.079	α = 90
b = 49.421	β = 90
c = 160.895	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-09-11 
Deposition Author(s): Mei, X.W., Chang, Y.G.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-09-11
  Type: Initial release