4M29

Structure of a GH39 Beta-xylosidase from Caulobacter crescentus

• PDB DOI: https://doi.org/10.2210/pdb4M29/pdb

• Classification: HYDROLASE
• Organism(s): Caulobacter vibrioides CB15
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-08-05 Released: 2013-08-14 
• Deposition Author(s): Polo, C.C., Santos, C.R., Correa, J.M., Simao, R.C.G., Seixas, F.A.V., Murakami, M.T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.286 
• R-Value Work: 0.228 
• R-Value Observed: 0.231 

Starting Model: experimental

Literature

Structure of a GH39 Beta-xylosidase from Caulobacter crescentus

Polo, C.C., Santos, C.R., Correa, J.M., Simao, R.C.G., Seixas, F.A.V., Murakami, M.T.

(null) Thesis 

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 56.5 kDa 
• Atom Count: 3,719 
• Modelled Residue Count: 443 
• Deposited Residue Count: 500 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-xylosidase	A	500	Caulobacter vibrioides CB15	Mutation(s): 0  Gene Names: Itgav, CC_2357
UniProt
Find proteins for Q9A5U0 (Caulobacter vibrioides (strain ATCC 19089 / CIP 103742 / CB 15)) Explore Q9A5U0  Go to UniProtKB:  Q9A5U0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MES	B [auth A]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.286 
• R-Value Work: 0.228 
• R-Value Observed: 0.231 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.287	α = 90
b = 57.347	β = 91.38
c = 94.05	γ = 90

Software Package:

Software Name	Purpose
NatXray	data collection
PHASER	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-08-14 
Deposition Author(s): Polo, C.C., Santos, C.R., Correa, J.M., Simao, R.C.G., Seixas, F.A.V., Murakami, M.T.

Revision History  

• Version 1.0: 2013-08-14
  Type: Initial release
  
• Version 1.1: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description