3SCY

Crystal structure of a putative 6-phosphogluconolactonase (BF1038) from Bacteroides fragilis NCTC 9343 at 1.50 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3SCY/pdb

• Classification: HYDROLASE
• Organism(s): Bacteroides fragilis NCTC 9343
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-06-08 Released: 2011-07-20 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.185 
• R-Value Work: 0.164 
• R-Value Observed: 0.165 

Literature

Crystal structure of a Hypothetical bacterial 6-phosphogluconolactonase (BF1038) from Bacteroides fragilis NCTC 9343 at 1.50 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: 39.36 kDa 
• Atom Count: 3,144 
• Modelled Residue Count: 356 
• Deposited Residue Count: 361 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical bacterial 6-phosphogluconolactonase	A	361	Bacteroides fragilis NCTC 9343	Mutation(s): 0  Gene Names: BF1038
UniProt
Find proteins for Q5LGG4 (Bacteroides fragilis (strain ATCC 25285 / DSM 2151 / CCUG 4856 / JCM 11019 / LMG 10263 / NCTC 9343 / Onslow / VPI 2553 / EN-2)) Explore Q5LGG4  Go to UniProtKB:  Q5LGG4

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	C [auth A], D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA	E [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N
UNL	B [auth A]	Unknown ligand FKNQFGJONOIPTF-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: 1.50 Å
• R-Value Free: 0.185 
• R-Value Work: 0.164 
• R-Value Observed: 0.165 
• Space Group: P 3₂ 2 1
• Diffraction Data: https://doi.org/10.18430/M33SCY

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.463	α = 90
b = 49.463	β = 90
c = 216.435	γ = 120

Software Package:

Software Name	Purpose
MolProbity	model building
PDB_EXTRACT	data extraction
SHELX	phasing
SHARP	phasing
XSCALE	data scaling
BUSTER-TNT	refinement
XDS	data reduction
SHELXD	phasing
BUSTER	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-07-20 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2011-07-20
  Type: Initial release
  
• Version 1.1: 2014-12-24
  Changes: Structure summary
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2023-02-01
  Changes: Database references, Derived calculations