6XPG

Crystal Structure of Sialate O-acetylesterase from Bacteroides vulgatus by Serial Crystallography

• PDB DOI: https://doi.org/10.2210/pdb6XPG/pdb

• Classification: HYDROLASE
• Organism(s): Phocaeicola vulgatus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-07-08 Released: 2020-07-15 
• Deposition Author(s): Kim, Y., Sherrell, D.A., Owen, R., Axford, D., Ebrahim, A., Johnson, J., Welk, L., Babnigg, G., 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: 1.90 Å
• R-Value Free: 
  0.242 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.206 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.208 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Sialate O-acetylesterase from Bacteroides vulgatus by Serial Crystallography

Kim, Y., Sherrell, D.A., Owen, R., Axford, D., Ebrahim, A., Johnson, J., Welk, L., Babnigg, G., Joachimiak, A.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 23.16 kDa 
• Atom Count: 1,645 
• Modelled Residue Count: 198 
• Deposited Residue Count: 202 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysophospholipase L1	A	202	Phocaeicola vulgatus	Mutation(s): 0  Gene Names: DW857_02595, DW869_04095, DWX04_04065, DWZ06_04430, DXA04_10705, EAJ12_11850, ERS852457_01148, ERS852509_00617, ERS852556_01195, SAMN04487923_100221 EC: 3
UniProt
Find proteins for A6L7S9 (Phocaeicola vulgatus (strain ATCC 8482 / DSM 1447 / JCM 5826 / CCUG 4940 / NBRC 14291 / NCTC 11154)) Explore A6L7S9  Go to UniProtKB:  A6L7S9

Small Molecules

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: 1.90 Å
• R-Value Free:  0.242 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.206 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.208 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.533	α = 90
b = 102.533	β = 90
c = 103.042	γ = 120

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-07-15 
Deposition Author(s): Kim, Y., Sherrell, D.A., Owen, R., Axford, D., Ebrahim, A., Johnson, J., Welk, L., Babnigg, G., 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	--

Revision History  

• Version 1.0: 2020-07-15
  Type: Initial release
  
• Version 1.1: 2020-12-23
  Changes: Database references, Structure summary
• Version 1.2: 2023-10-18
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2023-11-15
  Changes: Data collection
• Version 1.4: 2024-11-20
  Changes: Structure summary