7QAR | pdb_00007qar

Serial crystallography structure of cofactor-free urate oxidase in complex with the 5-peroxo derivative of 9-methyl uric acid at room temperature

• PDB DOI: https://doi.org/10.2210/pdb7QAR/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Aspergillus flavus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2021-11-17 Released: 2023-04-26 
• Deposition Author(s): Bui, S., Catapano, L., Zielinski, K., Yefanov, O., Murshudov, G.N., Oberthuer, D., Steiner, R.A.
• Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.266 (Depositor), 0.266 (DCC) 
• R-Value Work: 
  0.218 (Depositor), 0.222 (DCC) 

Starting Model: experimental

Literature

Rapid and efficient room-temperature serial synchrotron crystallography using the CFEL TapeDrive.

Zielinski, K.A., Prester, A., Andaleeb, H., Bui, S., Yefanov, O., Catapano, L., Henkel, A., Wiedorn, M.O., Lorbeer, O., Crosas, E., Meyer, J., Mariani, V., Domaracky, M., White, T.A., Fleckenstein, H., Sarrou, I., Werner, N., Betzel, C., Rohde, H., Aepfelbacher, M., Chapman, H.N., Perbandt, M., Steiner, R.A., Oberthuer, D.

(2022) IUCrJ 9: 778-791

• PubMed: 36381150 
• DOI: https://doi.org/10.1107/S2052252522010193
• Primary Citation Related Structures: 
  7QAR, 7ZPV, 7ZQ0, 8AF4, 8AF5, 8AF6, 8AF7, 8AF8


• PubMed Abstract: 
  

  Serial crystallography at conventional synchrotron light sources (SSX) offers the possibility to routinely collect data at room temperature using micrometre-sized crystals of biological macromolecules. However, SSX data collection is not yet as routine and currently takes significantly longer than the standard rotation series cryo-crystallography. Thus, its use for high-throughput approaches, such as fragment-based drug screening, where the possibility to measure at physio-logical temperatures would be a great benefit, is impaired. On the way to high-throughput SSX using a conveyor belt based sample delivery system - the CFEL TapeDrive - with three different proteins of biological relevance ( Klebsiella pneumoniae CTX-M-14 β-lactamase, Nectria haematococca xylanase GH11 and Aspergillus flavus urate oxidase), it is shown here that complete datasets can be collected in less than a minute and only minimal amounts of sample are required.

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Organizational Affiliation: 
• Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany.
Institute for Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246 Hamburg, Germany.
Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, University of Hamburg, c/o DESY, Building 22a, Notkestr. 85, 22603 Hamburg, Germany.
Randall Centre of Cell and Molecular Biophysics, King's College London, United Kingdom.
MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom.
Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany.
Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany.
Department of Physics, University of Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany.
Department of Biomedical Sciences, University of Padova, via Ugo Bassi 58/B, Padova 35131, Italy.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 34.5 kDa 
• Atom Count: 2,574 
• Modeled Residue Count: 295 
• Deposited Residue Count: 302 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uricase	A [auth AAA]	302	Aspergillus flavus	Mutation(s): 0  Gene Names: uaZ, uox EC: 1.7.3.3
UniProt
Find proteins for Q00511 (Aspergillus flavus) Explore Q00511  Go to UniProtKB:  Q00511

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
XDS (Subject of Investigation/LOI)	B [auth AAA]	(5S)-5-(dioxidanyl)-9-methyl-7H-purine-2,6,8-trione C6 H6 N4 O5 JQXTWGOGXIASQD-LURJTMIESA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.266 (Depositor), 0.266 (DCC) 
• R-Value Work:  0.218 (Depositor), 0.222 (DCC) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.79	α = 90
b = 96.03	β = 90
c = 105.21	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CrystFEL	data reduction
CrystFEL	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-04-26 
Deposition Author(s): Bui, S., Catapano, L., Zielinski, K., Yefanov, O., Murshudov, G.N., Oberthuer, D., Steiner, R.A.

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Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/P000169/1

Revision History  

• Version 1.0: 2023-04-26
  Type: Initial release
  
• Version 1.1: 2024-02-07
  Changes: Data collection, Refinement description