2G8L

Crystal structure of a duf89 family protein (ph1575) from pyrococcus horikoshii at 2.04 A resolution

• PDB DOI: https://doi.org/10.2210/pdb2G8L/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Pyrococcus horikoshii
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2006-03-02 Released: 2006-03-21 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.04 Å
• R-Value Free: 0.182 
• R-Value Work: 0.144 
• R-Value Observed: 0.146 

Literature

Crystal structure of hypothetical protein (3258004) from Pyrococcus horikoshii at 2.04 A resolution

Joint Center for Structural Genomics (JCSG)

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)

Biological Assembly Evidence: gel filtration, light scattering

Macromolecule Content

• Total Structure Weight: 69.37 kDa 
• Atom Count: 4,855 
• Modelled Residue Count: 571 
• Deposited Residue Count: 598 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
287aa long hypothetical protein	A, B	299	Pyrococcus horikoshii	Mutation(s): 9  Gene Names: 3258004
UniProt
Find proteins for O59272 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)) Explore O59272  Go to UniProtKB:  O59272

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	D [auth A], E [auth A], F [auth A], H [auth B], I [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
UNL	C [auth A], G [auth B]	Unknown ligand LYCAIKOWRPUZTN-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.04 Å
• R-Value Free: 0.182 
• R-Value Work: 0.144 
• R-Value Observed: 0.146 
• Space Group: P 3₁
• Diffraction Data: https://doi.org/10.18430/M32G8L

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.859	α = 90
b = 88.859	β = 90
c = 81.499	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SHELX	phasing
autoSHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-03-21 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2006-03-21
  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: 2017-10-25
  Changes: Author supporting evidence
• Version 1.4: 2023-01-25
  Changes: Database references, Derived calculations