6Y8G

selenomethionine derivative of ferulic acid esterase (FAE)

• PDB DOI: https://doi.org/10.2210/pdb6Y8G/pdb

• Classification: HYDROLASE
• Organism(s): Acetivibrio thermocellus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-03-04 Released: 2020-05-20 
• Deposition Author(s): von Stetten, D., Mueller-Dieckmann, C., Carpentier, P., Flot, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.200 
• R-Value Work: 0.175 

Literature

ID30A-3 (MASSIF-3) - a beamline for macromolecular crystallography at the ESRF with a small intense beam.

von Stetten, D., Carpentier, P., Flot, D., Beteva, A., Caserotto, H., Dobias, F., Guijarro, M., Giraud, T., Lentini, M., McSweeney, S., Royant, A., Petitdemange, S., Sinoir, J., Surr, J., Svensson, O., Theveneau, P., Leonard, G.A., Mueller-Dieckmann, C.

(2020) J Synchrotron Radiat 27: 844-851

• PubMed: 32381789 
• DOI: https://doi.org/10.1107/S1600577520004002
• Primary Citation of Related Structures:  
  6SWV, 6Y8G


• PubMed Abstract: 
  

  ID30A-3 (or MASSIF-3) is a mini-focus (beam size 18 µm × 14 µm) highly intense (2.0 × 10 ¹³  photons s ^-1 ), fixed-energy (12.81 keV) beamline for macromolecular crystallography (MX) experiments at the European Synchrotron Radiation Facility (ESRF). MASSIF-3 is one of two fixed-energy beamlines sited on the first branch of the canted undulator setup on the ESRF ID30 port and is equipped with a MD2 micro-diffractometer, a Flex HCD sample changer, and an Eiger X 4M fast hybrid photon-counting detector. MASSIF-3 is recommended for collecting diffraction data from single small crystals (≤15 µm in one dimension) or for experiments using serial methods. The end-station has been in full user operation since December 2014, and here its current characteristics and capabilities are described.

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Organizational Affiliation: 

European Synchrotron Radiation Facility, 71 Avenue des Martyrs, 38000 Grenoble, France.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 69.52 kDa 
• Atom Count: 5,040 
• Modelled Residue Count: 564 
• Deposited Residue Count: 594 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endo-1,4-beta-xylanase Y	A [auth AAA], B [auth BBB]	297	Acetivibrio thermocellus	Mutation(s): 0  Gene Names: xynY EC: 3.2.1.8
UniProt
Find proteins for P51584 (Acetivibrio thermocellus) Explore P51584  Go to UniProtKB:  P51584

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CD	C [auth AAA], D [auth AAA], E [auth AAA], F [auth BBB], G [auth BBB], H [auth BBB], I [auth BBB], J [auth BBB]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N
GOL	K [auth BBB]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A [auth AAA], B [auth BBB]	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET
SEP	A [auth AAA], B [auth BBB]	L-PEPTIDE LINKING	C3 H8 N O6 P		SER

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.200 
• R-Value Work: 0.175 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.519	α = 90
b = 108.373	β = 90
c = 112.949	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
SHELXDE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-05-20 
Deposition Author(s): von Stetten, D., Mueller-Dieckmann, C., Carpentier, P., Flot, D.

Revision History  

• Version 1.0: 2020-05-20
  Type: Initial release
  
• Version 1.1: 2020-06-03
  Changes: Advisory
• Version 1.2: 2023-03-01
  Changes: Advisory, Database references, Derived calculations