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- PDB-2n98: Solution structure of acyl carrier protein LipD from Actinoplanes... -

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Basic information

Entry
Database: PDB / ID: 2n98
TitleSolution structure of acyl carrier protein LipD from Actinoplanes friuliensis
ComponentsAcyl carrier protein
KeywordsTRANSPORT PROTEIN / acyl carrier protein
Function / homology
Function and homology information


phosphopantetheine binding
Similarity search - Function
ACP-like / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Acyl carrier protein
Similarity search - Component
Biological speciesActinoplanes friuliensis (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsPaul, S. / Ishida, H. / Liu, Z. / Nguyen, L.T. / Vogel, H.J.
CitationJournal: Protein Sci. / Year: 2017
Title: Structural and dynamic characterization of a freestanding acyl carrier protein involved in the biosynthesis of cyclic lipopeptide antibiotics.
Authors: Paul, S. / Ishida, H. / Nguyen, L.T. / Liu, Z. / Vogel, H.J.
History
DepositionNov 10, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Nov 16, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 15, 2017Group: Database references
Revision 1.2May 17, 2017Group: Database references
Revision 1.3Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Acyl carrier protein


Theoretical massNumber of molelcules
Total (without water)9,5051
Polymers9,5051
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)30 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Acyl carrier protein /


Mass: 9504.627 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Actinoplanes friuliensis (bacteria) / Gene: lipD / Plasmid: pET15MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q4H1C9

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
2223D HNCO
2323D HN(CA)CB
2423D CBCA(CO)NH
2523D HN(CA)CO
2623D HBHA(CO)NH
2723D H(CCO)NH
2823D C(CO)NH
1913D 1H-15N NOESY
31033D 1H-13C NOESY
41142D 1H-1H TOCSY
41242D DQF-COSY
41342D 1H-1H NOESY
5145IPAP-1H-15N-HSQC
31532D 1H-13C HSQC aromatic
1161IPAP-1H-15N-HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5 mM [U-15N] protein, 0.03 % sodium azide, 100 mM potassium chloride, 10 mM DTT, 0.5 mM DSS, 50 mM potassium phosphate, 90% H2O/10% D2O90% H2O/10% D2O
20.5 mM [U-13C; U-15N] protein, 100 mM potassium chloride, 10 mM DTT, 0.03 % sodium azide, 0.5 mM DSS, 50 mM potassium phosphate, 90% H2O/10% D2O90% H2O/10% D2O
30.5 mM [U-13C; U-15N] protein, 50 mM potassium phosphate, 100 mM potassium chloride, 10 mM DTT, 0.03 % sodium azide, 0.5 mM DSS, 100% D2O100% D2O
41 mM protein, 50 mM potassium phosphate, 100 mM potassium chloride, 0.03 % sodium azide, 10 mM DTT, 0.5 mM DSS, 100% D2O100% D2O
50.5 mM [U-15N] protein, 130 mM potassium chloride, 50 mM potassium phosphate, 10 mM DTT, 0.5 mM DSS, 0.03 % PMSF, 15 mg/mL Pf1 phage, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMentity-1[U-15N]1
0.03 %sodium azide-31
100 mMpotassium chloride-41
10 mMDTT-51
0.5 mMDSS-61
50 mMpotassium phosphate-71
0.5 mMentity-8[U-13C; U-15N]2
100 mMpotassium chloride-92
10 mMDTT-102
0.03 %sodium azide-112
0.5 mMDSS-132
50 mMpotassium phosphate-142
0.5 mMentity-15[U-13C; U-15N]3
50 mMpotassium phosphate-163
100 mMpotassium chloride-173
10 mMDTT-183
0.03 %sodium azide-193
0.5 mMDSS-203
1 mMentity-214
50 mMpotassium phosphate-224
100 mMpotassium chloride-234
0.03 %sodium azide-244
10 mMDTT-254
0.5 mMDSS-264
0.5 mMentity-27[U-15N]5
130 mMpotassium chloride-295
50 mMpotassium phosphate-305
10 mMDTT-315
0.5 mMDSS-325
0.03 %PMSF-335
15 mg/mLPf1 phage-345
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1100 6.0 ambient 297 K
2100 6.0 ambient 297 K
3100 6.4 ambient 297 K
4100 6.4 ambient 297 K
5130 ambient 297 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE5001
Bruker AvanceBrukerAVANCE7002
Bruker AvanceBrukerAVANCE6003

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2Guntert, Mumenthaler and Wuthrichchemical shift assignment
CYANA2Guntert, Mumenthaler and Wuthrichstructure solution
X-PLOR NIH2.19Schwieters, Kuszewski, Tjandra and Clorerefinement
X-PLOR NIH2.19Schwieters, Kuszewski, Tjandra and Clorestructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 30

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