3CED

Crystal structure of the C-terminal NIL domain of an ABC transporter protein homologue from Staphylococcus aureus

• PDB DOI: https://doi.org/10.2210/pdb3CED/pdb

• Classification: HYDROLASE
• Organism(s): Staphylococcus aureus subsp. aureus Mu50
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2008-02-28 Released: 2008-05-13 
• Deposition Author(s): Cuff, M.E., Bigelow, L., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.215 
• R-Value Work: 0.184 
• R-Value Observed: 0.186 

Literature

The structure of the C-terminal NIL domain of an ABC transporter protein homologue from Staphylococcus aureus.

Cuff, M.E., Bigelow, L., Clancy, S., Joachimiak, A.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 33.42 kDa 
• Atom Count: 2,731 
• Modelled Residue Count: 294 
• Deposited Residue Count: 294 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Methionine import ATP-binding protein metN 2	A, B, C	98	Staphylococcus aureus subsp. aureus Mu50	Mutation(s): 0  Gene Names: metN2, SAV0837 EC: 3.6.3 (PDB Primary Data), 7.4.2.11 (UniProt)
UniProt
Find proteins for Q99VG8 (Staphylococcus aureus (strain Mu50 / ATCC 700699)) Explore Q99VG8  Go to UniProtKB:  Q99VG8

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BU1	D [auth A], E [auth A], F [auth C], G [auth C]	1,4-BUTANEDIOL C4 H10 O2 WERYXYBDKMZEQL-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.215 
• R-Value Work: 0.184 
• R-Value Observed: 0.186 
• Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 132.55	α = 90
b = 132.55	β = 90
c = 132.083	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MLPHARE	phasing
DM	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
SHELXD	phasing
SHELXE	model building
SOLVE	phasing
RESOLVE	phasing
ARP/wARP	model building
CCP4	phasing
O	model building
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-05-13 
Deposition Author(s): Cuff, M.E., Bigelow, L., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2008-05-13
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Source and taxonomy, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2024-10-16
  Changes: Data collection, Database references, Derived calculations, Structure summary