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- PDB-1dv5: TERTIARY STRUCTURE OF APO-D-ALANYL CARRIER PROTEIN -

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Basic information

Entry
Database: PDB / ID: 1dv5
TitleTERTIARY STRUCTURE OF APO-D-ALANYL CARRIER PROTEIN
ComponentsAPO-D-ALANYL CARRIER PROTEIN
KeywordsTRANSPORT 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
D-alanyl carrier protein / ACP-like / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
D-alanyl carrier protein
Similarity search - Component
Biological speciesLactobacillus casei (bacteria)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsVolkman, 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
DepositionJan 19, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 1, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Nov 6, 2019Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / pdbx_database_related ...atom_site / pdbx_database_related / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _pdbx_database_related.db_id / _pdbx_nmr_software.name
Revision 2.1Apr 10, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: APO-D-ALANYL CARRIER PROTEIN


Theoretical massNumber of molelcules
Total (without water)8,7961
Polymers8,7961
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)30 / 50target function
Representative

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Components

#1: Protein APO-D-ALANYL CARRIER PROTEIN / APO-DCP


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

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1223D 13C-separated NOESY
1312D 15N-filtered NOESY
NMR detailsText: Complete resonance assignments obtained with triple-resonance NMR data as described in the primary citation.

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Sample preparation

Details
Solution-IDContentsSolvent system
11.2 mM [U-15N]apo-Dcp, 50 mM phosphate buffer90% H2O/10% D2O
21.8 mM [U-15N,13C]apo-Dcp, 50 mM phosphate buffer90% H2O/10% D2O
Sample conditionsIonic strength: 50 mM phosphate / pH: 5.8 / Pressure: ambient / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
Felix95Molecular Simulationsprocessing
NMRPipeFrank Delaglioprocessing
DYANA1.5Peter Guntertrefinement
XwinNMR2.3Brukercollection
XEASY1.3Bartelsdata analysis
RefinementMethod: 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 ensembleConformer selection criteria: target function / Conformers calculated total number: 50 / Conformers submitted total number: 30

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