4WBQ | pdb_00004wbq

Crystal structure of the exonuclease domain of QIP (QDE-2 interacting protein) solved by native-SAD phasing.

• PDB DOI: https://doi.org/10.2210/pdb4WBQ/pdb

• Classification: RNA BINDING PROTEIN
• Organism(s): Neurospora crassa
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-09-03 Released: 2014-12-10 
• Deposition Author(s): Boland, A., Weinert, T., Weichenrieder, O., Wang, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.69 Å
• R-Value Free: 
  0.227 (Depositor), 0.225 (DCC) 
• R-Value Work: 
  0.172 (Depositor), 0.179 (DCC) 
• R-Value Observed: 
  0.175 (Depositor) 

Literature

Fast native-SAD phasing for routine macromolecular structure determination.

Weinert, T., Olieric, V., Waltersperger, S., Panepucci, E., Chen, L., Zhang, H., Zhou, D., Rose, J., Ebihara, A., Kuramitsu, S., Li, D., Howe, N., Schnapp, G., Pautsch, A., Bargsten, K., Prota, A.E., Surana, P., Kottur, J., Nair, D.T., Basilico, F., Cecatiello, V., Pasqualato, S., Boland, A., Weichenrieder, O., Wang, B.C., Steinmetz, M.O., Caffrey, M., Wang, M.

(2015) Nat Methods 12: 131-133

• PubMed: 25506719 
• DOI: https://doi.org/10.1038/nmeth.3211
• Primary Citation Related Structures: 
  4PGO, 4PII, 4R8T, 4R8U, 4TN8, 4TNO, 4WAB, 4WAU, 4WBQ, 4WBX


• PubMed Abstract: 
  

  We describe a data collection method that uses a single crystal to solve X-ray structures by native SAD (single-wavelength anomalous diffraction). We solved the structures of 11 real-life examples, including a human membrane protein, a protein-DNA complex and a 266-kDa multiprotein-ligand complex, using this method. The data collection strategy is suitable for routine structure determination and can be implemented at most macromolecular crystallography synchrotron beamlines.

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Organizational Affiliation: 
• Swiss Light Source at Paul Scherrer Institut, Villigen, Switzerland.
Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, USA.
Laboratory of Biological Chemistry, Faculty of Applied Biological Sciences, Gifu University, Gifu, Japan.
Department of Biological Sciences, Graduate School of Science, Osaka University, Osaka, Japan.
Membrane Structural and Functional Biology Group, School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Dublin, Ireland.
Boehringer Ingelheim Pharma GmbH and Co. KG, Biberach an der Riss, Germany.
Laboratory of Biomolecular Research, Department of Biology and Chemistry, Paul Scherrer Institut, Villigen, Switzerland.
National Centre for Biological Sciences, Bangalore, India.
Department of Experimental Oncology, European Institute of Oncology, Milan, Italy.
Department of Biochemistry, Max Planck Institute for Developmental Biology, Tübingen, Germany.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 53.75 kDa 
• Atom Count: 2,766 
• Modeled Residue Count: 347 
• Deposited Residue Count: 480 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
QDE-2-interacting protein	A, B	240	Neurospora crassa	Mutation(s): 0
UniProt
Find proteins for A5JQJ3 (Neurospora crassa) Explore A5JQJ3  Go to UniProtKB:  A5JQJ3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	C [auth A], D [auth A], E [auth B], F [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.69 Å
• R-Value Free:  0.227 (Depositor), 0.225 (DCC) 
• R-Value Work:  0.172 (Depositor), 0.179 (DCC) 
• R-Value Observed: 0.175 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.04	α = 90
b = 77.04	β = 90
c = 112.31	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
SHELXDE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-12-10 
Deposition Author(s): Boland, A., Weinert, T., Weichenrieder, O., Wang, M.

Revision History  

• Version 1.0: 2014-12-10
  Type: Initial release
  
• Version 1.1: 2014-12-31
  Changes: Database references
• Version 1.2: 2015-02-11
  Changes: Database references
• Version 1.3: 2024-05-08
  Changes: Data collection, Database references, Derived calculations