1YD7 | pdb_00001yd7

Conserved hypothetical protein Pfu-1647980-001 from Pyrococcus furiosus

• PDB DOI: https://doi.org/10.2210/pdb1YD7/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Pyrococcus furiosus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2004-12-23 Released: 2005-02-08 
• Deposition Author(s): Horanyi, P., Florence, Q., Zhou, W., Chang, J., Zhao, M., Habel, J., Xu, H., Chen, L., Lee, D., Nguyen, D., Chang, S.-H., Tempel, W., Lin, D., Zhang, H., Praissman, J., Jenney Jr., F.E., Adams, M.W.W., Liu, Z.-J., 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: 
  0.243 (Depositor), 0.253 (DCC) 
• R-Value Work: 
  0.206 (Depositor), 0.215 (DCC) 
• R-Value Observed: 
  0.208 (Depositor) 

Literature

Conserved hypothetical protein Pfu-1647980-001 from Pyrococcus furiosus

Horanyi, P., Florence, Q., Zhou, W., Chang, J., Zhao, M., Habel, J., Xu, H., Chen, L., Lee, D., Nguyen, D., Chang, S.-H., Tempel, W., Lin, D., Zhang, H., Praissman, J., Jenney Jr., F.E., Adams, M.W.W., Liu, Z.-J., Rose, J.P., Wang, B.-C., Southeast Collaboratory for Structural Genomics (SECSG)

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 44.66 kDa 
• Atom Count: 1,310 
• Modeled Residue Count: 169 
• 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	395	Pyrococcus furiosus	Mutation(s): 12  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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UNX	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A]	UNKNOWN ATOM OR ION X

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.243 (Depositor), 0.253 (DCC) 
• R-Value Work:  0.206 (Depositor), 0.215 (DCC) 
• R-Value Observed: 0.208 (Depositor) 

Space Group: P 3₂ 1 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.448	α = 90
b = 61.448	β = 90
c = 129.084	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
RESOLVE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-02-08 
Deposition Author(s): Horanyi, P., Florence, Q., Zhou, W., Chang, J., Zhao, M., Habel, J., Xu, H., Chen, L., Lee, D., Nguyen, D., Chang, S.-H., Tempel, W., Lin, D., Zhang, H., Praissman, J., Jenney Jr., F.E., Adams, M.W.W., Liu, Z.-J., Rose, J.P., Wang, B.-C., Southeast Collaboratory for Structural Genomics (SECSG)

Revision History  

• Version 1.0: 2005-02-08
  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: 2017-10-11
  Changes: Refinement description
• Version 1.4: 2024-03-06
  Changes: Data collection, Database references, Derived calculations
• Version 1.5: 2024-11-20
  Changes: Structure summary