7D5G | pdb_00007d5g

Crystal structure of the CsCE with ligand to have a insight into the catalytic mechanism

• PDB DOI: https://doi.org/10.2210/pdb7D5G/pdb

• Classification: PROTEIN BINDING
• Organism(s): Caldicellulosiruptor saccharolyticus DSM 8903
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2020-09-25 Released: 2021-12-01 
• Deposition Author(s): Yang, R.J., Feng, Y.H., Andrew, J.F.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.202 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.166 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.168 (Depositor) 

Starting Model: experimental

Literature

A precise swaying map for how promiscuous cellobiose-2-epimerase operate bi-reaction

Feng, Y., Lyu, X., Cong, Y., Miao, T., Fang, B., Zhang, C., Shen, Q., Matthews, M., Fisher, A.J., Zhang, J.Z., Zhang, L., Yang, R.

(2023) Int J Biol Macromol 253: 127093

• DOI: https://doi.org/10.1016/j.ijbiomac.2023.127093

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 46.92 kDa 
• Atom Count: 3,764 
• Modeled Residue Count: 389 
• Deposited Residue Count: 389 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cellobiose 2-epimerase	A	389	Caldicellulosiruptor saccharolyticus DSM 8903	Mutation(s): 0  Gene Names: Csac_0294 EC: 5.1.3.11
UniProt
Find proteins for A4XGA6 (Caldicellulosiruptor saccharolyticus (strain ATCC 43494 / DSM 8903 / Tp8T 6331)) Explore A4XGA6  Go to UniProtKB:  A4XGA6

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-glucopyranose-(1-4)-beta-D-fructofuranose	B	2		N/A
Glycosylation Resources
GlyTouCan:  G92389FV GlyCosmos:  G92389FV

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL (Subject of Investigation/LOI)	C [auth A], D [auth A], E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.202 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.166 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.168 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.729	α = 90
b = 90.729	β = 90
c = 97.723	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-12-01 
Deposition Author(s): Yang, R.J., Feng, Y.H., Andrew, J.F.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	31771912

Revision History  

• Version 1.0: 2021-12-01
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description
• Version 1.2: 2024-11-13
  Changes: Database references, Structure summary