3NPG

Crystal structure of a protein with unknown function from DUF364 family (PH1506) from PYROCOCCUS HORIKOSHII at 2.70 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3NPG/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Pyrococcus horikoshii
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-06-28 Released: 2010-09-29 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.235 
• R-Value Work: 0.204 
• R-Value Observed: 0.206 

Literature

Crystal structure of a protein with unknown function from DUF364 family (PH1506) from PYROCOCCUS HORIKOSHII at 2.70 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 114.16 kDa 
• Atom Count: 7,609 
• Modelled Residue Count: 980 
• Deposited Residue Count: 996 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
uncharacterized DUF364 family protein	A, B, C, D	249	Pyrococcus horikoshii	Mutation(s): 0  Gene Names: PH1506
UniProt
Find proteins for O59175 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)) Explore O59175  Go to UniProtKB:  O59175

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACT	E [auth A], F [auth B], G [auth C], H [auth D]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.235 
• R-Value Work: 0.204 
• R-Value Observed: 0.206 
• Space Group: P 2₁ 2₁ 2₁
• Diffraction Data: https://doi.org/10.18430/M33NPG

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.541	α = 90
b = 95.179	β = 90
c = 159.098	γ = 90

Software Package:

Software Name	Purpose
MolProbity	model building
BUSTER-TNT	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction
Rosetta	phasing
PHASER	phasing
BUSTER	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-09-29 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2010-09-29
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2023-02-01
  Changes: Database references, Derived calculations
• Version 1.4: 2023-09-20
  Changes: Data collection, Refinement description
• Version 1.5: 2023-11-22
  Changes: Data collection