4H35 | pdb_00004h35

Feruloyl Esterase Domain of XYNY from Clostridium thermocellum before exposure to 266nm UV laser

• PDB DOI: https://doi.org/10.2210/pdb4H35/pdb

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


• Deposited: 2012-09-13 Released: 2012-12-12 
• Deposition Author(s): Pereira, P.J.B., de Sanctis, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.177 (Depositor), 0.178 (DCC) 
• R-Value Work: 
  0.157 (Depositor), 0.159 (DCC) 
• R-Value Observed: 
  0.159 (Depositor) 

Literature

In-house UV radiation-damage-induced phasing of selenomethionine-labeled protein structures.

Pereira, P.J., Royant, A., Panjikar, S., de Sanctis, D.

(2013) J Struct Biol 181: 89-94

• PubMed: 23178456 
• DOI: https://doi.org/10.1016/j.jsb.2012.11.003
• Primary Citation Related Structures: 
  4BAG, 4BAI, 4BAJ, 4H35


• PubMed Abstract: 
  

  Selenomethionine labeling is the most common technique used in protein crystallography to derivatize recombinant proteins for experimental phasing using anomalous scattering at tunable synchrotron beamlines. Recently, it has been shown that UV radiation depletes electron density of selenium atoms of selenomethionine residues and that UV radiation-damage-induced phasing (equivalent to single isomorphous replacement) protocol can be applied to calculate experimental phases. Here we present the straightforward integration of a UV source with an in-house diffractometer. We show how this setup can extend the capabilities of a sealed tube X-ray generator and be used for experimental phasing of selenium-labeled proteins.

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Organizational Affiliation: 
• IBMC-Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua do Campo Alegre 823, 4150-180 Porto, Portugal.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 69.43 kDa 
• Atom Count: 4,917 
• Modeled Residue Count: 566 
• 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, B	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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CD	C [auth A], D [auth A], E [auth A], F [auth A], G [auth B], H [auth B], I [auth B], J [auth B]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.177 (Depositor), 0.178 (DCC) 
• R-Value Work:  0.157 (Depositor), 0.159 (DCC) 
• R-Value Observed: 0.159 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.37	α = 90
b = 108.4	β = 90
c = 112.86	γ = 90

Software Package:

Software Name	Purpose
CrysalisPro	data collection
SHELXD	phasing
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-12-12 
Deposition Author(s): Pereira, P.J.B., de Sanctis, D.

Revision History  

• Version 1.0: 2012-12-12
  Type: Initial release
  
• Version 1.1: 2013-02-20
  Changes: Database references
• Version 1.2: 2017-11-15
  Changes: Refinement description
• Version 1.3: 2024-11-27
  Changes: Data collection, Database references, Derived calculations, Structure summary