1YEM

Conserved hypothetical protein Pfu-838710-001 from Pyrococcus furiosus

• PDB DOI: https://doi.org/10.2210/pdb1YEM/pdb
• Entry: 1YEM supersedes: 1XKC

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


• Deposited: 2004-12-28 Released: 2005-01-11 
• Deposition Author(s): Yang, H., Chang, J., Shah, A., Ng, J.D., Liu, Z.-J., Chen, L., Lee, D., Tempel, W., Praissman, J.L., Lin, D., Arendall III, W.B., Richardson, J.S., Richardson, D.C., Jenney Jr., F.E., Adams, M.W.W., Rose, J.P., 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: 
  0.258 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.223 (Depositor), 0.240 (DCC) 
• R-Value Observed: 
  0.225 (Depositor) 

Literature

Conserved hypothetical protein Pfu-838710-001 from Pyrococcus furiosus

Yang, H., Chang, J., Shah, A., Ng, J.D., Liu, Z.-J., Chen, L., Lee, D., Tempel, W., Praissman, J.L., Lin, D., Arendall III, W.B., Richardson, J.S., Richardson, D.C., Jenney Jr., F.E., Adams, M.W.W., Rose, J.P., Wang, B.-C.

To be published.

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: 43.03 kDa 
• Atom Count: 2,721 
• Modelled Residue Count: 329 
• Deposited Residue Count: 358 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Conserved hypothetical protein Pfu-838710-001	A, B	179	Pyrococcus furiosus DSM 3638	Mutation(s): 0  Gene Names: PF0863
UniProt
Find proteins for Q8U2H2 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)) Explore Q8U2H2  Go to UniProtKB:  Q8U2H2

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PT	C [auth A]	PLATINUM (II) ION Pt HRGDZIGMBDGFTC-UHFFFAOYSA-N
UNX	D [auth A], E [auth A], F [auth A], G [auth A], H [auth B], I [auth B], J [auth B]	UNKNOWN ATOM OR ION X

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.258 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.223 (Depositor), 0.240 (DCC) 
• R-Value Observed: 0.225 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.016	α = 90
b = 97.016	β = 90
c = 127.59	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
RESOLVE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-01-11 
Deposition Author(s): Yang, H., Chang, J., Shah, A., Ng, J.D., Liu, Z.-J., Chen, L., Lee, D., Tempel, W., Praissman, J.L., Lin, D., Arendall III, W.B., Richardson, J.S., Richardson, D.C., Jenney Jr., F.E., Adams, M.W.W., Rose, J.P., Wang, B.-C., Southeast Collaboratory for Structural Genomics (SECSG)
• This entry supersedes: 1XKC

Revision History  

• Version 1.0: 2005-01-11
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-06-28
  Changes: Database references, Source and taxonomy, Structure summary
• Version 1.4: 2017-10-11
  Changes: Refinement description
• Version 1.5: 2024-02-14
  Changes: Data collection, Database references, Derived calculations