+Open data
-Basic information
Entry | Database: PDB / ID: 1dv5 | |||||||||
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Title | TERTIARY STRUCTURE OF APO-D-ALANYL CARRIER PROTEIN | |||||||||
Components | APO-D-ALANYL CARRIER PROTEIN | |||||||||
Keywords | TRANSPORT PROTEIN / 3-helix bundle | |||||||||
Function / homology | Function and homology information D-alanyl carrier activity / lipoteichoic acid biosynthetic process / cell wall organization / cytoplasm Similarity search - Function | |||||||||
Biological species | Lactobacillus casei (bacteria) | |||||||||
Method | SOLUTION NMR / torsion angle dynamics | |||||||||
Authors | Volkman, B.F. / Zhang, Q. / Debabov, D.V. / Rivera, E. / Kresheck, G.C. / Neuhaus, F.C. | |||||||||
Citation | Journal: Biochemistry / Year: 2001 Title: Biosynthesis of D-alanyl-lipoteichoic acid: the tertiary structure of apo-D-alanyl carrier protein. Authors: Volkman, B.F. / Zhang, Q. / Debabov, D.V. / Rivera, E. / Kresheck, G.C. / Neuhaus, F.C. #1: Journal: J.Bacteriol. / Year: 1996 Title: The D-Alanyl Carrier Protein in Lactobacillus casei: Cloning, Sequencing and Expression of dltC Authors: Debabov, D.V. / Heaton, M.P. / Zhang, Q. / Stewart, K.D. / Lambalot, R.H. / Neuhaus, F.C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1dv5.cif.gz | 709.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dv5.ent.gz | 595.5 KB | Display | PDB format |
PDBx/mmJSON format | 1dv5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dv/1dv5 ftp://data.pdbj.org/pub/pdb/validation_reports/dv/1dv5 | HTTPS FTP |
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-Related structure data
Related structure data | 1hqbC C: citing same article (ref.) |
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Similar structure data | |
Other databases |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 8795.818 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-81 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactobacillus casei (bacteria) / Plasmid: PDCP1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3 / References: UniProt: P55153 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||
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NMR experiment |
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NMR details | Text: Complete resonance assignments obtained with triple-resonance NMR data as described in the primary citation. |
-Sample preparation
Details |
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Sample conditions | Ionic strength: 50 mM phosphate / pH: 5.8 / Pressure: ambient / Temperature: 298 K | |||||||||
Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
NMR spectrometer | Type: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 600 MHz |
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-Processing
NMR software |
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Refinement | Method: torsion angle dynamics / Software ordinal: 1 Details: The structures are based on a total of 1582 non-trivial upper-limit distance constraints (332 long-range, 560 medium-range, 372 sequential and 318 intraresidue), derived from 3288 assigned ...Details: The structures are based on a total of 1582 non-trivial upper-limit distance constraints (332 long-range, 560 medium-range, 372 sequential and 318 intraresidue), derived from 3288 assigned NOEs from 4 2D and 3D spectra. This corresponds to an average of 19.8 constraints/residue. No additional constraints were included. Structures were generated using the ANNEAL function of the program DYANA 1.5, with 8000 torsion angle dynamics steps for each structure. The average DYANA target function for the 30 conformers was 0.68 +/- 0.11. The average backbone atomic RMSD to the mean structure for residues 4-81 is 0.43 +/- 0.08 Angstroms, and 0.86 +/- 0.09 for all non-hydrogen atoms (residues 4-81). | ||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: target function / Conformers calculated total number: 50 / Conformers submitted total number: 30 |