5C0P | pdb_00005c0p

The crystal structure of endo-arabinase from Bacteroides thetaiotaomicron VPI-5482

• PDB DOI: https://doi.org/10.2210/pdb5C0P/pdb

• Classification: HYDROLASE
• Organism(s): Bacteroides thetaiotaomicron VPI-5482
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-06-12 Released: 2015-07-01 
• Deposition Author(s): Tan, K., Cuff, M., Joachimiak, G., Endres, M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.53 Å
• R-Value Free: 
  0.164 (Depositor), 0.164 (DCC) 
• R-Value Work: 
  0.149 (Depositor), 0.149 (DCC) 
• R-Value Observed: 
  0.150 (Depositor) 

Literature

The crystal structure of endo-arabinase from Bacteroides thetaiotaomicron VPI-5482

Tan, K., Cuff, M., Joachimiak, G., Endres, M., Joachimiak, A.

To be published.

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: 34.33 kDa 
• Atom Count: 2,605 
• Modeled Residue Count: 284 
• Deposited Residue Count: 298 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endo-arabinase	A	298	Bacteroides thetaiotaomicron VPI-5482	Mutation(s): 0  Gene Names: BT_1873
UniProt
Find proteins for Q8A6K8 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50)) Explore Q8A6K8  Go to UniProtKB:  Q8A6K8

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TRS	J [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
GOL	F [auth A], G [auth A], H [auth A], I [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	D [auth A], E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	B [auth A], C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.53 Å
• R-Value Free:  0.164 (Depositor), 0.164 (DCC) 
• R-Value Work:  0.149 (Depositor), 0.149 (DCC) 
• R-Value Observed: 0.150 (Depositor) 

Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.804	α = 90
b = 83.804	β = 90
c = 43.366	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
MLPHARE	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2015-07-01 
Deposition Author(s): Tan, K., Cuff, M., Joachimiak, G., Endres, M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM094585

Revision History  

• Version 1.0: 2015-07-01
  Type: Initial release
  
• Version 1.1: 2017-09-27
  Changes: Advisory, Author supporting evidence, Derived calculations, Source and taxonomy, Structure summary
• Version 1.2: 2019-12-25
  Changes: Author supporting evidence
• Version 1.3: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary