6FJ4 | pdb_00006fj4

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 
    0.178 (Depositor), 0.204 (DCC) 
  • R-Value Work: 
    0.160 (Depositor), 0.193 (DCC) 
  • R-Value Observed: 
    0.161 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 6FJ4

This is version 1.3 of the entry. See complete history. 

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

  • DOI: https://doi.org/10.1107/S1600577518007166
  • Primary Citation 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).

    • Organizational Affiliation: 
    • European Molecular Biology Laboratory, Grenoble Outstation, 71 avenue des Martyrs, Grenoble 38042, France.

Macromolecule Content 

  • Total Structure Weight: 33.6 kDa 
  • Atom Count: 2,533 
  • Modeled Residue Count: 283 
  • Deposited Residue Count: 283 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:
|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Endo-1,4-beta-xylanase Y283Acetivibrio thermocellusMutation(s): 0 
Gene Names: xynY
EC: 3.2.1.8
UniProt
Find proteins for P51584 (Acetivibrio thermocellus)
Explore P51584 
Go to UniProtKB:  P51584
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP51584
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
SEP
Query on SEP
A
L-PEPTIDE LINKINGC3 H8 N O6 PSER

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free:  0.178 (Depositor), 0.204 (DCC) 
  • R-Value Work:  0.160 (Depositor), 0.193 (DCC) 
  • R-Value Observed: 0.161 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 112.023α = 90
b = 112.023β = 90
c = 65.865γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MxCuBEdata collection
XDSdata reduction
Aimlessdata scaling
CRANK2phasing

Structure Validation

View Full Validation Report



View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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
  • Version 1.3: 2024-11-06
    Changes: Data collection, Database references, Derived calculations, Structure summary