4PII

Crystal structure of hypothetical protein PF0907 from pyrococcus furiosus solved by sulfur SAD using Swiss light source data

• PDB DOI: https://doi.org/10.2210/pdb4PII/pdb

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


• Deposited: 2014-05-08 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: 2.17 Å
• R-Value Free: 0.234 
• R-Value Work: 0.173 
• R-Value Observed: 0.179 

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 of 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.

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: 29.69 kDa 
• Atom Count: 1,989 
• Modelled Residue Count: 239 
• Deposited Residue Count: 250 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
N-glycosylase/DNA lyase	A	250	Pyrococcus furiosus DSM 3638	Mutation(s): 0  Gene Names: PF0904 EC: 3.2.2 (PDB Primary Data), 4.2.99.18 (PDB Primary Data)
UniProt
Find proteins for Q8U2D5 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)) Explore Q8U2D5  Go to UniProtKB:  Q8U2D5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IMD	K [auth A]	IMIDAZOLE C3 H5 N2 RAXXELZNTBOGNW-UHFFFAOYSA-O
CL	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.17 Å
• R-Value Free: 0.234 
• R-Value Work: 0.173 
• R-Value Observed: 0.179 
• Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.43	α = 90
b = 98.43	β = 90
c = 65.23	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data reduction
SHELXDE	phasing
Coot	model building
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling

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: Database references
• Version 1.2: 2017-11-22
  Changes: Derived calculations, Refinement description
• Version 1.3: 2023-12-27
  Changes: Data collection, Database references