2PK8 | pdb_00002pk8

Crystal structure of an uncharacterized protein PF0899 from Pyrococcus furiosus

• PDB DOI: https://doi.org/10.2210/pdb2PK8/pdb
• Entry: 2PK8 supersedes: 1SHE

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


• Deposited: 2007-04-17 Released: 2007-05-22 
• Deposition Author(s): Liu, Z.J., Tempel, W., Chen, L., Shah, A., Lee, D., Clancy-Kelley, L.L., Dillard, B.D., Rose, J.P., Sugar, F.J., Jenny Jr., F.E., Lee, H.S., Izumi, M., Shah, C., Poole III, F.L., Adams, M.W.W., Richardson, J.S., Richardson, D.C., Wang, B.-C., Southeast Collaboratory for Structural Genomics (SECSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.242 (Depositor), 0.241 (DCC) 
• R-Value Work: 
  0.207 (Depositor), 0.205 (DCC) 
• R-Value Observed: 
  0.208 (Depositor) 

Literature

Structure of the hypothetical protein PF0899 from Pyrococcus furiosus at 1.85 A resolution.

Kelley, L.L., Dillard, B.D., Tempel, W., Chen, L., Shaw, N., Lee, D., Newton, M.G., Sugar, F.J., Jenney, F.E., Lee, H.S., Shah, C., Poole, F.L., Adams, M.W., Richardson, J.S., Richardson, D.C., Liu, Z.J., Wang, B.C., Rose, J.

(2007) Acta Crystallogr Sect F Struct Biol Cryst Commun 63: 549-552

• PubMed: 17620707 
• DOI: https://doi.org/10.1107/S1744309107024049
• Primary Citation Related Structures: 
  2PK8


• PubMed Abstract: 
  

  The hypothetical protein PF0899 is a 95-residue peptide from the hyperthermophilic archaeon Pyrococcus furiosus that represents a gene family with six members. P. furiosus ORF PF0899 has been cloned, expressed and crystallized and its structure has been determined by the Southeast Collaboratory for Structural Genomics (http://www.secsg.org). The structure was solved using the SCA2Structure pipeline from multiple data sets and has been refined to 1.85 A against the highest resolution data set collected (a presumed gold derivative), with a crystallographic R factor of 21.0% and R(free) of 24.0%. The refined structure shows some structural similarity to a wedge-shaped domain observed in the structure of the major capsid protein from bacteriophage HK97, suggesting that PF0899 may be a structural protein.

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Organizational Affiliation: 
• Southeast Collaboratory for Structural Genomics, Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 11.82 kDa 
• Atom Count: 784 
• Modeled Residue Count: 94 
• Deposited Residue Count: 103 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein PF0899	A	103	Pyrococcus furiosus DSM 3638	Mutation(s): 0  Gene Names: PF0899
UniProt
Find proteins for Q8U2E0 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)) Explore Q8U2E0  Go to UniProtKB:  Q8U2E0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AUC	B [auth A]	GOLD (I) CYANIDE ION C2 Au N2 DGOHFTDNMSZWDQ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.242 (Depositor), 0.241 (DCC) 
• R-Value Work:  0.207 (Depositor), 0.205 (DCC) 
• R-Value Observed: 0.208 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.08	α = 90
b = 47.08	β = 90
c = 83.95	γ = 120

Software Package:

Software Name	Purpose
SOLVE	phasing
REFMAC	refinement
SERGUI	data collection
MAR345	data collection
SCALEPACK	data scaling
SCA2structure	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-05-22 
Deposition Author(s): Liu, Z.J., Tempel, W., Chen, L., Shah, A., Lee, D., Clancy-Kelley, L.L., Dillard, B.D., Rose, J.P., Sugar, F.J., Jenny Jr., F.E., Lee, H.S., Izumi, M., Shah, C., Poole III, F.L., Adams, M.W.W., Richardson, J.S., Richardson, D.C., Wang, B.-C., Southeast Collaboratory for Structural Genomics (SECSG)
• This entry supersedes: 1SHE

Revision History  

• Version 1.0: 2007-05-22
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2018-01-24
  Changes: Structure summary
• Version 1.5: 2024-02-21
  Changes: Data collection, Database references, Derived calculations