1YBZ

Conserved hypothetical protein from Pyrococcus furiosus Pfu-1581948-001

• PDB DOI: https://doi.org/10.2210/pdb1YBZ/pdb

• Classification: ISOMERASE
• Organism(s): Pyrococcus furiosus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2004-12-21 Released: 2005-02-01 
• Deposition Author(s): Lee, D., Chen, L., Nguyen, D., Dillard, B.D., Tempel, W., Habel, J., Zhou, W., Chang, S.-H., Kelley, L.-L.C., Liu, Z.-J., Lin, D., Zhang, H., Praissman, J., Bridger, S., Eneh, J.C., Hopkins, R.C., Jenney Jr., F.E., Lee, H.-S., Li, T., Poole II, F.L., Shah, C., Sugar, F.J., 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: 1.82 Å
• R-Value Free: 0.237 
• R-Value Work: 0.201 
• R-Value Observed: 0.203 

Literature

Conserved hypothetical protein from Pyrococcus furiosus Pfu-1581948-001

Lee, D., Chen, L., Nguyen, D., Dillard, B.D., Tempel, W., Habel, J., Zhou, W., Chang, S.-H., Kelley, L.-L.C., Liu, Z.-J., Lin, D., Zhang, H., Praissman, J., Bridger, S., Eneh, J.C., Hopkins, R.C., Jenney Jr., F.E., Lee, H.-S., Li, T., Poole II, F.L., Shah, C., Sugar, F.J., Adams, M.W.W., Rose, J.P., Wang, B.-C.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 generated by PISA,PQS (software)

Macromolecule Content

• Total Structure Weight: 10.87 kDa 
• Atom Count: 664 
• Modelled Residue Count: 76 
• Deposited Residue Count: 91 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
chorismate mutase	A	91	Pyrococcus furiosus	Mutation(s): 0  EC: 5.4.99.5
UniProt
Find proteins for Q8U098 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)) Explore Q8U098  Go to UniProtKB:  Q8U098

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.82 Å
• R-Value Free: 0.237 
• R-Value Work: 0.201 
• R-Value Observed: 0.203 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.501	α = 90
b = 52.501	β = 90
c = 80.217	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
RESOLVE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
ARP/wARP	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-02-01 
Deposition Author(s): Lee, D., Chen, L., Nguyen, D., Dillard, B.D., Tempel, W., Habel, J., Zhou, W., Chang, S.-H., Kelley, L.-L.C., Liu, Z.-J., Lin, D., Zhang, H., Praissman, J., Bridger, S., Eneh, J.C., Hopkins, R.C., Jenney Jr., F.E., Lee, H.-S., Li, T., Poole II, F.L., Shah, C., Sugar, F.J., Adams, M.W.W., Rose, J.P., Wang, B.-C., Southeast Collaboratory for Structural Genomics (SECSG)

Revision History  

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