6XPM | pdb_00006xpm

Crystal Structure of Sialate O-acetylesterase from Bacteroides vulgatus with microfluidics crystals at room temperature

• PDB DOI: https://doi.org/10.2210/pdb6XPM/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., Johnson, J., Welk, L., Endres, M., Levens, A., Sherrell, D.A., 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: 2.30 Å
• R-Value Free: 
  0.184 (Depositor), 0.192 (DCC) 
• R-Value Work: 
  0.149 (Depositor), 0.154 (DCC) 
• R-Value Observed: 
  0.150 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Sialate O-acetylesterase from Bacteroides vulgatus with microfluidics crystals at room temperature

Kim, Y., Johnson, J., Welk, L., Endres, M., Levens, A., Sherrell, D.A., 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: 22.99 kDa 
• Atom Count: 1,606 
• Modeled Residue Count: 197 
• 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

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NA	B [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.184 (Depositor), 0.192 (DCC) 
• R-Value Work:  0.149 (Depositor), 0.154 (DCC) 
• R-Value Observed: 0.150 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.627	α = 90
b = 102.627	β = 90
c = 102.834	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., Johnson, J., Welk, L., Endres, M., Levens, A., Sherrell, D.A., 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