4FFD | pdb_00004ffd

Crystal structure of engineered protein. northeast structural genomics consortium target or48

• PDB DOI: https://doi.org/10.2210/pdb4FFD/pdb

• Classification: Structural Genomics, Unknown Function
• Organism(s): Pyrococcus horikoshii
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-05-31 Released: 2013-02-13 
• Deposition Author(s): Seetharaman, J., Lew, S., Nivon, L., Baker, D., Bjelic, S., Ciccosanti, C., Sahdev, S., Xiao, R., Everett, J.K., Acton, T.B., Montelione, G.T., Tong, L., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.31 Å
• R-Value Free: 
  0.279 (Depositor), 0.277 (DCC) 
• R-Value Work: 
  0.238 (Depositor), 0.238 (DCC) 
• R-Value Observed: 
  0.238 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of engineered protein. northeast structural genomics consortium target or48

Seetharaman, J., Lew, S., Nivon, L., Baker, D., Bjelic, S., Ciccosanti, C., Sahdev, S., Xiao, R., Everett, J.K., Acton, T.B., Montelione, G.T., Tong, L., Hunt, J.F.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 26.63 kDa 
• Atom Count: 1,901 
• Modeled Residue Count: 230 
• Deposited Residue Count: 234 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PF00702 DOMAIN PROTEIN	A	234	Pyrococcus horikoshii	Mutation(s): 0
UniProt
Find proteins for O58216 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)) Explore O58216  Go to UniProtKB:  O58216

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.31 Å
• R-Value Free:  0.279 (Depositor), 0.277 (DCC) 
• R-Value Work:  0.238 (Depositor), 0.238 (DCC) 
• R-Value Observed: 0.238 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.334	α = 90
b = 71.367	β = 104.83
c = 52.926	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
AMoRE	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-02-13 
Deposition Author(s): Seetharaman, J., Lew, S., Nivon, L., Baker, D., Bjelic, S., Ciccosanti, C., Sahdev, S., Xiao, R., Everett, J.K., Acton, T.B., Montelione, G.T., Tong, L., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

Revision History  

• Version 1.0: 2013-02-13
  Type: Initial release
  
• Version 1.1: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description