6FJ4

Structure of FAE solved by SAD from data collected at the peak of the Selenium absorption edge on ID30B

• PDB DOI:  https://doi.org/10.2210/pdb6FJ4/pdb

• Classification: HYDROLASE
• Organism(s): Acetivibrio thermocellus
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2018-01-19 Released: 2018-02-07 
• Deposition Author(s): McCarthy, A.A., Mueller-Dieckmann, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.178 
• R-Value Work: 0.160 
• R-Value Observed: 0.161 

Literature

ID30B - a versatile beamline for macromolecular crystallography experiments at the ESRF.

McCarthy, A.A., Barrett, R., Beteva, A., Caserotto, H., Dobias, F., Felisaz, F., Giraud, T., Guijarro, M., Janocha, R., Khadrouche, A., Lentini, M., Leonard, G.A., Lopez Marrero, M., Malbet-Monaco, S., McSweeney, S., Nurizzo, D., Papp, G., Rossi, C., Sinoir, J., Sorez, C., Surr, J., Svensson, O., Zander, U., Cipriani, F., Theveneau, P., Mueller-Dieckmann, C.

(2018) J Synchrotron Radiat 25: 1249-1260

• PubMed: 29979188 
• DOI: https://doi.org/10.1107/S1600577518007166
• Primary Citation of Related Structures:  
  6FID, 6FJ2, 6FJ4, 6FJ6, 6FJ8, 6FJ9


• PubMed Abstract: 
  

ID30B is an undulator-based high-intensity, energy-tuneable (6.0-20 keV) and variable-focus (20-200 µm in diameter) macromolecular crystallography (MX) beamline at the ESRF. It was the last of the ESRF Structural Biology Group's beamlines to be constructed and commissioned as part of the ESRF's Phase I Upgrade Program and has been in user operation since June 2015. Both a modified microdiffractometer (MD2S) incorporating an in situ plate screening capability and a new flexible sample changer (the FlexHCD) were specifically developed for ID30B. Here, the authors provide the current beamline characteristics and detail how different types of MX experiments can be performed on ID30B (http://www.esrf.eu/id30b).

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Organizational Affiliation: 

European Synchrotron Radiation Facility, 71 avenue des Martyrs, Grenoble 38043, France.

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: 33.6 kDa 
• Atom Count: 2,533 
• Modelled Residue Count: 283 
• Deposited Residue Count: 283 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endo-1,4-beta-xylanase Y	A	283	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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CD	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N
SO4	I [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	G [auth A], H [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.178 
• R-Value Work: 0.160 
• R-Value Observed: 0.161 
• Space Group: P 4₁ 2₁ 2
• Diffraction Data: https://doi.org/10.15785/SBGRID/543

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.023	α = 90
b = 112.023	β = 90
c = 65.865	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MxCuBE	data collection
XDS	data reduction
Aimless	data scaling
CRANK2	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-02-07 
Deposition Author(s): McCarthy, A.A., Mueller-Dieckmann, C.

Revision History  

• Version 1.0: 2018-02-07
  Type: Initial release
  
• Version 1.1: 2018-07-18
  Changes: Data collection, Database references
• Version 1.2: 2018-08-08
  Changes: Data collection, Database references