3JYS

Crystal structure of SusD superfamily protein (YP_001298690.1) from Bacteroides vulgatus ATCC 8482 at 2.00 A resolution

• PDB DOI:  https://doi.org/10.2210/pdb3JYS/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Phocaeicola vulgatus ATCC 8482
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-09-22 Released: 2009-10-06 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.198 
• R-Value Work: 0.178 
• R-Value Observed: 0.179 

Literature

Crystal structure of SusD superfamily protein (YP_001298690.1) from Bacteroides vulgatus ATCC 8482 at 2.00 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: 56.84 kDa 
• Atom Count: 4,161 
• Modelled Residue Count: 479 
• Deposited Residue Count: 499 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SusD superfamily protein	A	499	Phocaeicola vulgatus ATCC 8482	Mutation(s): 0  Gene Names: BVU_1379, YP_001298690.1
UniProt
Find proteins for A6L054 (Phocaeicola vulgatus (strain ATCC 8482 / DSM 1447 / JCM 5826 / CCUG 4940 / NBRC 14291 / NCTC 11154)) Explore A6L054  Go to UniProtKB:  A6L054

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	B [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: 2.00 Å
• R-Value Free: 0.198 
• R-Value Work: 0.178 
• R-Value Observed: 0.179 
• Space Group: P 4₁ 2₁ 2
• Diffraction Data: https://doi.org/10.18430/M33JYS

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.929	α = 90
b = 63.929	β = 90
c = 266.398	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-10-06 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2009-10-06
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-11-01
  Changes: 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