3NKG | pdb_00003nkg

Crystal Structure of GEBA250068378 from Sulfurospirillum deleyianum

• PDB DOI: https://doi.org/10.2210/pdb3NKG/pdb

• Classification: structural genomics, unknown function
• Organism(s): Sulfurospirillum deleyianum DSM 6946
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2010-06-19 Released: 2010-08-18 
• Deposition Author(s): Kim, Y., Marshall, N., Cobb, G., Eisen, J., Kerfeld, C., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.214 (Depositor), 0.208 (DCC) 
• R-Value Work: 
  0.169 (Depositor), 0.165 (DCC) 
• R-Value Observed: 
  0.172 (Depositor) 

Literature

Crystal Structure of GEBA250068378 from Sulfurospirillum deleyianum

Kim, Y., Marshall, N., Cobb, G., Eisen, J., Kerfeld, C., Joachimiak, A.

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)

Biological Assembly 2  

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

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

Macromolecule Content 

• Total Structure Weight: 40.36 kDa 
• Atom Count: 3,135 
• Modeled Residue Count: 340 
• Deposited Residue Count: 348 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
uncharacterized protein GEBA250068378	A, B	174	Sulfurospirillum deleyianum DSM 6946	Mutation(s): 0  Gene Names: Sdel_1248
UniProt
Find proteins for D1B2F0 (Sulfurospirillum deleyianum (strain ATCC 51133 / DSM 6946 / 5175)) Explore D1B2F0  Go to UniProtKB:  D1B2F0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	D [auth A], G [auth A], J [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACY	C [auth A], E [auth A], F [auth A], H [auth B], I [auth B]	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-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: 2.00 Å
• R-Value Free:  0.214 (Depositor), 0.208 (DCC) 
• R-Value Work:  0.169 (Depositor), 0.165 (DCC) 
• R-Value Observed: 0.172 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.373	α = 90
b = 39.414	β = 95.45
c = 88.575	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	data collection
HKL-3000	phasing
SHELXS	phasing
MLPHARE	phasing
RESOLVE	model building
SOLVE	phasing
PHENIX	model building
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
RESOLVE	phasing
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-08-18 
Deposition Author(s): Kim, Y., Marshall, N., Cobb, G., Eisen, J., Kerfeld, C., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2010-08-18
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary