3LNL

Crystal structure of Staphylococcus aureus protein SA1388

• PDB DOI: https://doi.org/10.2210/pdb3LNL/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Staphylococcus aureus subsp. aureus N315
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2010-02-02 Released: 2010-03-16 
• Deposition Author(s): Singh, K.S., Chruszcz, M., Zhang, X., Minor, W., Zhang, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.191 
• R-Value Work: 0.149 
• R-Value Observed: 0.151 

Literature

Structure of a Conserved Hypothetical Protein Sa1388 from S. aureus Reveals a Capped Hexameric Toroid with Two Pii Domain Lids and a Dinuclear Metal Center.

Singh Saikatendu, K., Zhang, X., Kinch, L., Leybourne, M., Grishin, N.V., Zhang, H.

(2006) BMC Struct Biol 6: 27

• PubMed: 17187687 
• DOI: https://doi.org/10.1186/1472-6807-6-27
• Primary Citation of Related Structures:  
  2NYD, 3LNL


• PubMed Abstract: 
  

  The protein encoded by the SA1388 gene from Staphylococcus aureus was chosen for structure determination to elucidate its domain organization and confirm our earlier remote homology based prediction that it housed a nitrogen regulatory PII protein-like domain. SA1388 was predicted to contain a central PII-like domain and two flanking regions, which together belong to the NIF3-like protein family. Proteins like SA1388 remain a poorly studied group and their structural characterization could guide future investigations aimed at understanding their function.

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Organizational Affiliation: 

Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas TX 75390-8816, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

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

Macromolecule Content

• Total Structure Weight: 84.04 kDa 
• Atom Count: 5,914 
• Modelled Residue Count: 656 
• Deposited Residue Count: 740 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UPF0135 protein SA1388	A, B	370	Staphylococcus aureus subsp. aureus N315	Mutation(s): 2  Gene Names: SA1388
UniProt
Find proteins for P67273 (Staphylococcus aureus (strain N315)) Explore P67273  Go to UniProtKB:  P67273

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
B3P	E [auth A], H [auth B]	2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C11 H26 N2 O6 HHKZCCWKTZRCCL-UHFFFAOYSA-N
ZN	C [auth A], D [auth A], F [auth B], G [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.191 
• R-Value Work: 0.149 
• R-Value Observed: 0.151 
• Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 132.547	α = 90
b = 132.547	β = 90
c = 125.67	γ = 120

Software Package:

Software Name	Purpose
SBC-Collect	data collection
SOLVE	phasing
HKL-3000	phasing
REFMAC	refinement
Coot	model building
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-03-16 
Deposition Author(s): Singh, K.S., Chruszcz, M., Zhang, X., Minor, W., Zhang, H.

Revision History  

• Version 1.0: 2010-03-16
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2021-10-13
  Changes: Database references, Derived calculations
• Version 1.4: 2022-04-13
  Changes: Structure summary
• Version 1.5: 2024-02-21
  Changes: Data collection