4WBX | pdb_00004wbx

Conserved hypothetical protein PF1771 from Pyrococcus furiosus solved by sulfur SAD using Swiss Light Source data

• PDB DOI: https://doi.org/10.2210/pdb4WBX/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Pyrococcus furiosus DSM 3638
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-09-04 Released: 2014-12-10 
• Deposition Author(s): Weinert, T., Waltersperger, S., Olieric, V., Panepucci, E., Chen, L., Rose, J.P., Wang, M., Wang, B.C., Southeast Collaboratory for Structural Genomics (SECSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.277 (Depositor), 0.284 (DCC) 
• R-Value Work: 
  0.233 (Depositor), 0.241 (DCC) 
• R-Value Observed: 
  0.238 (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: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 44.1 kDa 
• Atom Count: 2,256 
• Modeled Residue Count: 298 
• Deposited Residue Count: 395 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2-keto acid:ferredoxin oxidoreductase subunit alpha	A [auth C]	395	Pyrococcus furiosus DSM 3638	Mutation(s): 0  Gene Names: PF1771 EC: 1.2.7.3
UniProt
Find proteins for Q8U046 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)) Explore Q8U046  Go to UniProtKB:  Q8U046

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.277 (Depositor), 0.284 (DCC) 
• R-Value Work:  0.233 (Depositor), 0.241 (DCC) 
• R-Value Observed: 0.238 (Depositor) 

Space Group: F 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.02	α = 90
b = 126.82	β = 90
c = 155.17	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
SHELXDE	phasing
BUSTER	refinement
Coot	model building
SHELX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-12-10 
Deposition Author(s): Weinert, T., Waltersperger, S., Olieric, V., Panepucci, E., Chen, L., Rose, J.P., Wang, M., Wang, B.C., Southeast Collaboratory for Structural Genomics (SECSG)

Revision History  

• Version 1.0: 2014-12-10
  Type: Initial release
  
• Version 1.1: 2015-08-12
  Changes: Other
• Version 1.2: 2017-11-22
  Changes: Derived calculations, Refinement description
• Version 1.3: 2018-01-24
  Changes: Other, Structure summary
• Version 1.4: 2023-12-27
  Changes: Data collection, Database references