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- PDB-2md9: Solution Structure of an Active Site Mutant Pepitdyl Carrier Protein -

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Basic information

Entry
Database: PDB / ID: 2md9
TitleSolution Structure of an Active Site Mutant Pepitdyl Carrier Protein
ComponentsTyrocidine synthase 3
KeywordsLIGASE / Protein / Carrier Protein
Function / homology
Function and homology information


amino acid activation for nonribosomal peptide biosynthetic process / secondary metabolite biosynthetic process / carboxylic acid metabolic process / phosphopantetheine binding / ligase activity / antibiotic biosynthetic process / cytosol
Similarity search - Function
ACP-like / PKS_PP_betabranch / Thioesterase / Thioesterase domain / Condensation domain / Condensation domain / Amino acid adenylation domain / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / AMP-binding enzyme, C-terminal domain / AMP-binding enzyme C-terminal domain ...ACP-like / PKS_PP_betabranch / Thioesterase / Thioesterase domain / Condensation domain / Condensation domain / Amino acid adenylation domain / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / AMP-binding enzyme, C-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding, conserved site / Chloramphenicol acetyltransferase-like domain superfamily / Putative AMP-binding domain signature. / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / AMP-dependent synthetase/ligase / AMP-binding enzyme, C-terminal domain superfamily / AMP-binding enzyme / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Alpha/Beta hydrolase fold / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Tyrocidine synthase 3
Similarity search - Component
Biological speciesBrevibacillus parabrevis (bacteria)
MethodSOLUTION NMR / molecular dynamics
Model detailsclosest to the average, model1
AuthorsTufar, P. / Rahighi, S. / Kraas, F.I. / Kirchner, D.K. / Loehr, F. / Henrich, E. / Koepke, J. / Dikic, I. / Guentert, P. / Marahiel, M.A. / Doetsch, V.
CitationJournal: Chem.Biol. / Year: 2014
Title: Crystal Structure of a PCP/Sfp Complex Reveals the Structural Basis for Carrier Protein Posttranslational Modification.
Authors: Tufar, P. / Rahighi, S. / Kraas, F.I. / Kirchner, D.K. / Lohr, F. / Henrich, E. / Kopke, J. / Dikic, I. / Guntert, P. / Marahiel, M.A. / Dotsch, V.
History
DepositionSep 6, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 23, 2014Provider: repository / Type: Initial release
Revision 1.1May 14, 2014Group: Database references
Revision 1.2Nov 29, 2017Group: Derived calculations / Category: struct_conf / struct_conf_type
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: Tyrocidine synthase 3


Theoretical massNumber of molelcules
Total (without water)9,9721
Polymers9,9721
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)20 / 100target function
RepresentativeModel #1closest to the average

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Components

#1: Protein Tyrocidine synthase 3 / Tyrocidine synthase III / ATP-dependent asparagine adenylase / AsnA / Asparagine activase / ATP- ...Tyrocidine synthase III / ATP-dependent asparagine adenylase / AsnA / Asparagine activase / ATP-dependent glutamine adenylase / GlnA / Glutamine activase / ATP-dependent tyrosine adenylase / TyrA / Tyrosine activase / ATP-dependent valine adenylase / ValA / Valine activase / ATP-dependent ornithine adenylase / OrnA / Ornithine activase / ATP-dependent leucine adenylase / LeuA / Leucine activase


Mass: 9972.424 Da / Num. of mol.: 1 / Fragment: Third PCP domain of TycC (UNP Residues 3032-3113) / Mutation: S45A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brevibacillus parabrevis (bacteria) / Strain: ATCC 8185 / Gene: tycC / Production host: Escherichia coli (E. coli) / Strain (production host): M15 / Variant (production host): pREP4 / References: UniProt: O30409

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC aliphatic
1312D 1H-13C HSQC aromatic
1413D HN(CA)CB
1513D H(CCCO)NH-TOCSY
1613D (H)C(CCO)NH-TOCSY
1713D 1H-15N NOESY
1813D 1H-13C NOESY aromatic

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Sample preparation

DetailsContents: 0.7 mM [U-100% 13C; U-100% 15N] PCP, 50 mM sodium phosphate, 0.15 mM DSS, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.7 mMPCP-1[U-100% 13C; U-100% 15N]1
50 mMsodium phosphate-21
0.15 mMDSS-31
Sample conditionspH: 6.8 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE9002

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Processing

NMR software
NameVersionDeveloperClassification
TALOSCornilescu, Delaglio and Baxgeometry optimization
Sparky3.114Goddardpeak picking
Sparky3.114Goddardchemical shift assignment
TopSpin3Bruker Biospincollection
TopSpin3Bruker Biospinprocessing
CYANA3.96Guntert, Mumenthaler and Wuthrichstructure solution
OPALp1.4Luginbuhl, Guntert, Billeter and Wuthrichrefinement
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 1419 / NOE intraresidue total count: 243 / NOE long range total count: 301 / NOE medium range total count: 457 / NOE sequential total count: 418 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 70 / Protein psi angle constraints total count: 70
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20 / Maximum torsion angle constraint violation: 3.63 ° / Maximum upper distance constraint violation: 0.13 Å
NMR ensemble rmsDistance rms dev: 0.0145 Å / Distance rms dev error: 0.0005 Å

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