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 | magnesium | crystallization |
| CL | chloride | 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
- 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)
- 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