8X8H | pdb_00008x8h

A carbohydrate binding domain of a putative pectate lyase

• PDB DOI: https://doi.org/10.2210/pdb8X8H/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Lachnoclostridium phytofermentans ISDg
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-11-27 Released: 2024-12-04 
• Deposition Author(s): Liu, G.C., Chang, Y.G.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.208 (Depositor), 0.209 (DCC) 
• R-Value Work: 
  0.162 (Depositor), 0.162 (DCC) 
• R-Value Observed: 
  0.163 (Depositor) 

Starting Model: in silico

Literature

Structure of a carbohydrate binding domain at 2.00 Angstroms resolution

Liu, G.C., 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 Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Macromolecule Content

• Total Structure Weight: 74.75 kDa 
• Atom Count: 5,082 
• Modelled Residue Count: 576 
• Deposited Residue Count: 696 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pectate disaccharide-lyase	A, B, C, D	174	Lachnoclostridium phytofermentans ISDg	Mutation(s): 0  Gene Names: Cphy_1888
UniProt
Find proteins for A9KT46 (Lachnoclostridium phytofermentans (strain ATCC 700394 / DSM 18823 / ISDg)) Explore A9KT46  Go to UniProtKB:  A9KT46

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.208 (Depositor), 0.209 (DCC) 
• R-Value Work:  0.162 (Depositor), 0.162 (DCC) 
• R-Value Observed: 0.163 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.1	α = 90
b = 81.1	β = 90
c = 251.942	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-12-04 
Deposition Author(s): Liu, G.C., Chang, Y.G.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-12-04
  Type: Initial release