3S5Q | pdb_00003s5q

Crystal structure of a putative glycosyl hydrolase (BDI_2473) from Parabacteroides distasonis ATCC 8503 at 1.85 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3S5Q/pdb

• Classification: HYDROLASE
• Organism(s): Parabacteroides distasonis ATCC 8503
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-05-23 Released: 2011-06-15 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.202 (Depositor), 0.216 (DCC) 
• R-Value Work: 
  0.169 (Depositor), 0.181 (DCC) 
• R-Value Observed: 
  0.171 (Depositor) 

Literature

Crystal structure of a Hypothetical Glycosyl hydrolase (BDI_2473) from Parabacteroides distasonis ATCC 8503 at 1.85 A resolution

Joint Center for Structural Genomics (JCSG)

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: 25.5 kDa 
• Atom Count: 1,970 
• Modeled Residue Count: 213 
• Deposited Residue Count: 214 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative glycosylhydrolase	A	214	Parabacteroides distasonis ATCC 8503	Mutation(s): 0  Gene Names: BDI_2473
UniProt
Find proteins for A6LES9 (Parabacteroides distasonis (strain ATCC 8503 / DSM 20701 / CIP 104284 / JCM 5825 / NCTC 11152)) Explore A6LES9  Go to UniProtKB:  A6LES9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IOD	B [auth A], C [auth A], D [auth A]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M
EDO	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-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: 1.85 Å
• R-Value Free:  0.202 (Depositor), 0.216 (DCC) 
• R-Value Work:  0.169 (Depositor), 0.181 (DCC) 
• R-Value Observed: 0.171 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33S5Q

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.062	α = 90
b = 60.473	β = 90
c = 77.221	γ = 90

Software Package:

Software Name	Purpose
MolProbity	model building
PDB_EXTRACT	data extraction
SHELX	phasing
SHARP	phasing
XSCALE	data scaling
REFMAC	refinement
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-06-15 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2011-06-15
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2014-12-24
  Changes: Structure summary
• Version 1.3: 2017-11-08
  Changes: Refinement description
• Version 1.4: 2024-10-09
  Changes: Data collection, Database references, Derived calculations, Structure summary