3HBK | pdb_00003hbk

Crystal structure of putative glycosyl hydrolase, was Domain of Unknown Function (DUF1080) (YP_001302580.1) from Parabacteroides distasonis ATCC 8503 at 2.36 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3HBK/pdb

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


• Deposited: 2009-05-04 Released: 2009-05-26 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.36 Å
• R-Value Free: 
  0.245 (Depositor), 0.247 (DCC) 
• R-Value Work: 
  0.198 (Depositor), 0.198 (DCC) 
• R-Value Observed: 
  0.200 (Depositor) 

Literature

Crystal structure of putative glycosyl hydrolase, was Domain of Unknown Function (DUF1080) (YP_001302580.1) from Parabacteroides distasonis ATCC 8503 at 2.36 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)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 27.66 kDa 
• Atom Count: 1,916 
• Modeled Residue Count: 231 
• Deposited Residue Count: 245 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
putative glycosyl hydrolase	A	245	Parabacteroides distasonis ATCC 8503	Mutation(s): 0  Gene Names: BDI_1195, YP_001302580.1
UniProt
Find proteins for A6LB94 (Parabacteroides distasonis (strain ATCC 8503 / DSM 20701 / CIP 104284 / JCM 5825 / NCTC 11152)) Explore A6LB94  Go to UniProtKB:  A6LB94

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A], C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	D [auth A], E [auth A], F [auth A], G [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: 2.36 Å
• R-Value Free:  0.245 (Depositor), 0.247 (DCC) 
• R-Value Work:  0.198 (Depositor), 0.198 (DCC) 
• R-Value Observed: 0.200 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33HBK

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.009	α = 90
b = 61.009	β = 90
c = 167.332	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-05-26 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2009-05-26
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Author supporting evidence, Refinement description
• Version 1.3: 2019-07-24
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.4: 2023-02-01
  Changes: Database references, Derived calculations
• Version 1.5: 2024-11-06
  Changes: Data collection, Structure summary