3BPD | pdb_00003bpd

Crystal structure of an uncharacterized protein (O28723_ARCFU) from Archaeoglobus fulgidus

• PDB DOI: https://doi.org/10.2210/pdb3BPD/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Archaeoglobus fulgidus DSM 4304
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2007-12-18 Released: 2008-01-08 
• Deposition Author(s): Eswaramoorthy, S., Burley, S.K., Sauder, J.M., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.305 (Depositor), 0.300 (DCC) 
• R-Value Work: 
  0.242 (Depositor), 0.240 (DCC) 

Starting Model: experimental

Literature

Crystal structure of an uncharacterized protein (O28723_ARCFU) from Archaeoglobus fulgidus.

Eswaramoorthy, S., Burley, S.K., Sauder, J.M., Swaminathan, S.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C7  (Explore in 3D)
Global Stoichiometry: Homo 7-mer - A7 

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

Biological Assembly 2  

Global Symmetry: Cyclic - C7  (Explore in 3D)
Global Stoichiometry: Homo 7-mer - A7 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 157.97 kDa 
• Atom Count: 9,922 
• Modeled Residue Count: 1,273 
• Deposited Residue Count: 1,400 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein	A, B, C, D, E, F, G, H, I, J, K, L, M, N	100	Archaeoglobus fulgidus DSM 4304	Mutation(s): 1  Gene Names: AF_1549
UniProt
Find proteins for O28723 (Archaeoglobus fulgidus (strain ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16)) Explore O28723  Go to UniProtKB:  O28723

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	AA [auth F], BA [auth F], CA [auth G], DA [auth G], EA [auth G], FA [auth G], GA [auth H], HA [auth I], IA [auth J], JA [auth K], KA [auth K], LA [auth K], MA [auth L], NA [auth L], O [auth A], OA [auth L], P [auth A], Q [auth A], R [auth B], S [auth B], T [auth C], U [auth C], V [auth C], W [auth D], X [auth E], Y [auth F], Z [auth F]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C, D, E, F, G, H, I, J, K, L, M, N	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.305 (Depositor), 0.300 (DCC) 
• R-Value Work:  0.242 (Depositor), 0.240 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.51	α = 90
b = 97.36	β = 90
c = 179.002	γ = 90

Software Package:

Software Name	Purpose
MAR345	data collection
MOLREP	phasing
CNS	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-01-08 
Deposition Author(s): Eswaramoorthy, S., Burley, S.K., Sauder, J.M., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2008-01-08
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2012-02-08
  Changes: Derived calculations
• Version 1.3: 2017-10-25
  Changes: Refinement description
• Version 1.4: 2018-11-14
  Changes: Data collection, Structure summary
• Version 1.5: 2021-02-03
  Changes: Database references, Derived calculations, Structure summary
• Version 1.6: 2021-10-20
  Changes: Database references
• Version 1.7: 2023-08-30
  Changes: Data collection, Refinement description
• Version 1.8: 2023-11-15
  Changes: Data collection
• Version 1.9: 2024-11-06
  Changes: Structure summary