8XMZ | pdb_00008xmz

Crystal structure of a novel porphyran-binding carbohydrate binding module

• PDB DOI: https://doi.org/10.2210/pdb8XMZ/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Aquimarina sp. BL5
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-12-28 Released: 2024-01-17 
• Deposition Author(s): Mei, X.W., Chang, Y.G.
• Funding Organization(s): Not funded

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.299 (Depositor), 0.310 (DCC) 
• R-Value Work: 
  0.260 (Depositor), 0.280 (DCC) 
• R-Value Observed: 
  0.264 (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 Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 36.64 kDa 
• Atom Count: 2,094 
• Modeled Residue Count: 274 
• Deposited Residue Count: 338 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
T9SS C-terminal target domain-containing protein	A, B	169	Aquimarina sp. BL5	Mutation(s): 0  Gene Names: D1818_19300

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.299 (Depositor), 0.310 (DCC) 
• R-Value Work:  0.260 (Depositor), 0.280 (DCC) 
• R-Value Observed: 0.264 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.614	α = 90
b = 95.614	β = 90
c = 215.531	γ = 120

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: 2024-01-17 
Deposition Author(s): Mei, X.W., Chang, Y.G.

---

Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-01-17
  Type: Initial release