5C6L | pdb_00005c6l

Crystal Structure of Gadolinium derivative of HEWL solved using intense Free-Electron Laser radiation

• PDB DOI: https://doi.org/10.2210/pdb5C6L/pdb

• Classification: HYDROLASE
• Organism(s): Gallus gallus
• Mutation(s): No 


• Deposited: 2015-06-23 Released: 2015-07-08 
• Deposition Author(s): Galli, L., Barends, T.R.M., Son, S.-K., White, T.A., Barty, A., Botha, S., Boutet, S., Caleman, C., Doak, R.B., Nanao, M.H., Nass, K., Shoeman, R.L., Timneanu, N., Santra, R., Schlichting, I., Chapman, H.N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.280 (Depositor), 0.276 (DCC) 
• R-Value Work: 
  0.219 (Depositor), 0.227 (DCC) 
• R-Value Observed: 
  0.222 (Depositor) 

Literature

Towards phasing using high X-ray intensity.

Galli, L., Son, S.K., Barends, T.R., White, T.A., Barty, A., Botha, S., Boutet, S., Caleman, C., Doak, R.B., Nanao, M.H., Nass, K., Shoeman, R.L., Timneanu, N., Santra, R., Schlichting, I., Chapman, H.N.

(2015) IUCrJ 2: 627-634

• PubMed: 26594370 
• DOI: https://doi.org/10.1107/S2052252515014049
• Primary Citation Related Structures: 
  5C6I, 5C6J, 5C6L


• PubMed Abstract: 
  

  X-ray free-electron lasers (XFELs) show great promise for macromolecular structure determination from sub-micrometre-sized crystals, using the emerging method of serial femtosecond crystallography. The extreme brightness of the XFEL radiation can multiply ionize most, if not all, atoms in a protein, causing their scattering factors to change during the pulse, with a preferential 'bleaching' of heavy atoms. This paper investigates the effects of electronic damage on experimental data collected from a Gd derivative of lysozyme microcrystals at different X-ray intensities, and the degree of ionization of Gd atoms is quantified from phased difference Fourier maps. A pattern sorting scheme is proposed to maximize the ionization contrast and the way in which the local electronic damage can be used for a new experimental phasing method is discussed.

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Organizational Affiliation: 
• Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY , Notkestrasse 85, Hamburg, 22607, Germany ; Department of Physics, University of Hamburg , Luruper Chaussee 149, Hamburg, 22761, Germany.
Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY , Notkestrasse 85, Hamburg, 22607, Germany ; The Hamburg Centre for Ultrafast Imaging , Luruper Chaussee 149, Hamburg, 22761, Germany.
Biomolecular Mechanisms, MPI for Medical Research , Jahnstrasse 29, Heidelberg, 69120, Germany.
Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY , Notkestrasse 85, Hamburg, 22607, Germany.
Max Planck Institute for Medical Research , Jahnstrasse 29, Heidelberg, 69120, Germany.
SLAC National Accelerator Laboratory , 2575 Sand Hill Road, Menlo Park, 94025, USA.
Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY , Notkestrasse 85, Hamburg, 22607, Germany ; Department of Physics and Astronomy, Uppsala University , Box 516, Uppsala, 75120, Sweden.
EMBL, Grenoble Outstation , Rue Jules Horowitz 6, Grenoble, 38042, France.
Department of Physics and Astronomy, Uppsala University , Box 516, Uppsala, 75120, Sweden ; Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University , Box 596, Uppsala, 75124, Sweden.
Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY , Notkestrasse 85, Hamburg, 22607, Germany ; The Hamburg Centre for Ultrafast Imaging , Luruper Chaussee 149, Hamburg, 22761, Germany ; Department of Physics, University of Hamburg , Juniungstrasse 6, Hamburg, 20355, Germany.
Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY , Notkestrasse 85, Hamburg, 22607, Germany ; Department of Physics, University of Hamburg , Luruper Chaussee 149, Hamburg, 22761, Germany ; The Hamburg Centre for Ultrafast Imaging , Luruper Chaussee 149, Hamburg, 22761, Germany.

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: 15.6 kDa 
• Atom Count: 1,063 
• Modeled Residue Count: 129 
• Deposited Residue Count: 129 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysozyme C	A	129	Gallus gallus	Mutation(s): 0  EC: 3.2.1.17
UniProt
Find proteins for P00698 (Gallus gallus) Explore P00698  Go to UniProtKB:  P00698

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DO3	B [auth A], C [auth A]	10-((2R)-2-HYDROXYPROPYL)-1,4,7,10-TETRAAZACYCLODODECANE 1,4,7-TRIACETIC ACID C17 H32 N4 O7 IQUHNCOJRJBMSU-CQSZACIVSA-N
GD	H [auth A], I [auth A]	GADOLINIUM ATOM Gd UIWYJDYFSGRHKR-UHFFFAOYSA-N
CL	D [auth A], E [auth A], F [auth A], G [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.280 (Depositor), 0.276 (DCC) 
• R-Value Work:  0.219 (Depositor), 0.227 (DCC) 
• R-Value Observed: 0.222 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.2	α = 90
b = 79.2	β = 90
c = 39.4	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SOLVE	phasing
ARP	model building
CrystFEL	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-07-08 
Deposition Author(s): Galli, L., Barends, T.R.M., Son, S.-K., White, T.A., Barty, A., Botha, S., Boutet, S., Caleman, C., Doak, R.B., Nanao, M.H., Nass, K., Shoeman, R.L., Timneanu, N., Santra, R., Schlichting, I., Chapman, H.N.

Revision History  

• Version 1.0: 2015-07-08
  Type: Initial release
  
• Version 1.1: 2015-12-09
  Changes: Database references
• Version 1.2: 2018-01-24
  Changes: Data collection
• Version 1.3: 2018-11-14
  Changes: Data collection
• Version 1.4: 2024-11-06
  Changes: Data collection, Database references, Structure summary