Structure of IDP91963

1.0 Angstrom resolution crystal structure of the branched-chain amino acid transporter substrate binding protein LivJ from Streptococcus pneumoniae str. Canada MDR_19A in complex with Isoleucine

Edit deposit information
CSGID target
IDP91963 
PDB Id
4GNR (NCBI MMDB
Authors
A.S.Halavaty,M.Kudritska,Z.Wawrzak,P.J.Stogios,V.Yim,A.Savchenko,W.F.Anderson,Center For Structural Genomics Of Infectious Diseases (Csgid) 
Responsible person
Andrei Halavaty 
Responsible lab
Northwestern University 
Deposition Date
Aug 17, 2012 
Release Date
Sep 05, 2012 

Annotation

Description
The 1.0 A resolution crystal structure of he branched-chain amino acid transporter substrate binding protein LivJ (construct 35–386) from Streptococcus pneumoniae str. Canada MDR_19A in complex with Isoleucine was determined by molecular replacement. The P21 asymmetric unit contains a single copy of the protein that is composed of two domains. The N-terminal domain spans residues 35–155 and residues 292–358 that fold into a parallel 5-stranded beta-sheet and 3 helices, and an antiparallel 2-stranded beta-sheet and 3 helices. The C-terminal domain encompasses residues 157–291 and residues 359–386. Isoleucine residue binds the protein at the interface of the two domains. The residue’s side chain is facing a hydrophobic pocket, whereas its main-chain charged atoms interact with polar residues of the protein. The N-terminal domain contains modified residue, N-dimethyl-lysine, at position 345 that is surface exposed and faces Asn342.  
Functional assignment
Transport protein 

Ligands

Ligand code Name Ligand type
MG crystallization
CL crystallization
175 3,5-dihydro-5-methylidene-4h-imidazol-4-on

Structure information

Unit cell parameters

Space Group
P 1 21 1  
Unit Cell

a=37.27Å, b=72.82Å, c=57.54Å
α=90.00, β=105.10, γ=90.00 
Solvent content
 
Matthews coefficient
 

Refinement

Data for the highest resolution shell is in parentheses.
Resolution range
27.78-1.00Å (1.03-1.00Å)  
Rall(%)
12.7 
Rwork(%)
12.6 (23.2) 
Rfree(%)
14.7 (24.8) 
Num. observed reflections
159062 (11635) 
Num. Rfree reflections
7953 (599) 
Completeness(%)
99.7 (98.7) 

Model parameters

Num Atoms
2926  
Num Waters
613  
Num Hetatoms
675  
Model mean isotropic B factor
9.150Å2  
RMSD bond length
0.012Å  
RMSD bond angle
1.747°  
Filename uploaded
4GNR.pdb (uploaded on Jun 05, 2015 11:45 AM)  
Inserted
Aug 17, 2012