4MDY

Crystal structure of periplasmic solute binding protein from Mycobacterium smegmatis str. MC2 155

• PDB DOI: https://doi.org/10.2210/pdb4MDY/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Mycolicibacterium smegmatis MC2 155
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-08-23 Released: 2013-09-04 
• Deposition Author(s): Chang, C., Wu, R., Endres, M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free: 0.201 
• R-Value Work: 0.146 
• R-Value Observed: 0.149 

Literature

Crystal structure of periplasmic solute binding protein from Mycobacterium smegmatis str. MC2 155

Chang, C., Wu, R., Endres, M., 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)

Macromolecule Content

• Total Structure Weight: 31.6 kDa 
• Atom Count: 2,398 
• Modelled Residue Count: 285 
• Deposited Residue Count: 295 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Periplasmic binding protein	A	295	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0  Gene Names: MSMEG_0438, MSMEI_0427
UniProt
Find proteins for A0QPL3 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0QPL3  Go to UniProtKB:  A0QPL3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	B [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free: 0.201 
• R-Value Work: 0.146 
• R-Value Observed: 0.149 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.606	α = 90
b = 90.449	β = 90
c = 33.974	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
MLPHARE	phasing
DM	phasing
SHELXDE	phasing
ARP/wARP	model building
RESOLVE	phasing
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-09-04 
Deposition Author(s): Chang, C., Wu, R., Endres, M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2013-09-04
  Type: Initial release
  
• Version 1.1: 2017-11-15
  Changes: Refinement description