4B96 | pdb_00004b96

Family 3b carbohydrate-binding module from the biomass sensoring system of Clostridium clariflavum

• PDB DOI: https://doi.org/10.2210/pdb4B96/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Acetivibrio clariflavus
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2012-09-02 Released: 2013-09-18 
• Deposition Author(s): Yaniv, O., Reddy, Y.H.K., Yoffe, H., Shimon, L.J.W., Bayer, E.A., Lamed, R., Frolow, F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.91 Å
• R-Value Free: 
  0.189 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.153 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.155 (Depositor) 

Starting Model: other

Literature

Structure of Cbm3B from the Biomass Sensoring System of Clostridium Clarifalvum

Yaniv, O., Reddy, Y.H.K., Bayer, E.A., Lamed, R., Frolow, F.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 18.17 kDa 
• Atom Count: 1,494 
• Modeled Residue Count: 151 
• Deposited Residue Count: 151 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CELLULOSE BINDING DOMAIN-CONTAINING PROTEIN	A	151	Acetivibrio clariflavus	Mutation(s): 0
UniProt
Find proteins for G8LST1 (Acetivibrio clariflavus (strain DSM 19732 / NBRC 101661 / EBR45)) Explore G8LST1  Go to UniProtKB:  G8LST1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	E [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	B [auth A], C [auth A], D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.91 Å
• R-Value Free:  0.189 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.153 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.155 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 135.212	α = 90
b = 135.212	β = 90
c = 54.323	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-09-18 
Deposition Author(s): Yaniv, O., Reddy, Y.H.K., Yoffe, H., Shimon, L.J.W., Bayer, E.A., Lamed, R., Frolow, F.

Revision History  

• Version 1.0: 2013-09-18
  Type: Initial release
  
• Version 1.1: 2024-05-01
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description