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- PDB-2mr8: holo structure of the Peptidyl Carrier Protein Domain 7 of the te... -

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Basic information

Entry
Database: PDB / ID: 2mr8
Titleholo structure of the Peptidyl Carrier Protein Domain 7 of the teicoplanin producing Non-ribosomal peptide synthetase
ComponentsNon-ribosomal peptide synthetase
KeywordsBIOSYNTHETIC PROTEIN / Non-ribosomal peptide synthetase / peptidyl carrier protein
Function / homology
Function and homology information


secondary metabolite biosynthetic process / lipid biosynthetic process / phosphopantetheine binding / catalytic activity
Similarity search - Function
Polyketide synthase, thioesterase domain / Thioesterase / ACP-like / Thioesterase / Thioesterase domain / Condensation domain / Condensation domain / Amino acid adenylation domain / ANL, N-terminal domain / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A ...Polyketide synthase, thioesterase domain / Thioesterase / ACP-like / Thioesterase / Thioesterase domain / Condensation domain / Condensation domain / Amino acid adenylation domain / ANL, N-terminal 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 / AMP-binding enzyme, C-terminal domain superfamily / 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
Non-ribosomal peptide synthetase
Similarity search - Component
Biological speciesActinoplanes teichomyceticus (bacteria)
MethodSOLUTION NMR / molecular dynamics
Model detailslowest energy, model 1
AuthorsHaslinger, K. / Maximowitsch, E. / Redfield, C. / Cryle, M.J.
CitationJournal: Proteins / Year: 2015
Title: Structure of the terminal PCP domain of the non-ribosomal peptide synthetase in teicoplanin biosynthesis.
Authors: Haslinger, K. / Redfield, C. / Cryle, M.J.
History
DepositionJul 2, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 28, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 8, 2015Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / 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 / _struct_ref_seq_dif.details
Revision 1.3May 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: Non-ribosomal peptide synthetase


Theoretical massNumber of molelcules
Total (without water)9,6311
Polymers9,6311
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 20all calculated structures submitted
RepresentativeModel #1lowest energy

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Components

#1: Protein Non-ribosomal peptide synthetase


Mass: 9631.036 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Actinoplanes teichomyceticus (bacteria)
Strain: 1867 / Gene: tcp12 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21gold (DE3) / References: UniProt: Q70AZ6

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1143D 1H-15N NOESY
1232D 1H-1H NOESY
1313D 1H-13C NOESY
1422D DQF-COSY
1542D 1H-15N HSQC
1612D 1H-13C HSQC
1713D CBCA(CO)NH
1813D HNCO
1913D HNCA
11013D HN(CA)CB
11113D HBHA(CO)NH
11213D HN(CO)CA
11313D (H)CCH-TOCSY
11413D HNCCCONH
11513D CBCANH
11622D 1H-1H TOCSY
11743D 1H-15N TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
1350-500 uM [U-100% 13C; U-100% 15N] PCP7T, 50 mM TRIS, 95% H2O/5% D2O95% H2O/5% D2O
2500 uM PCP7T, 50 mM TRIS, 95% H2O/5% D2O95% H2O/5% D2O
3500 uM PCP7T, 50 mM TRIS, 100% D2O100% D2O
4350-500 uM [U-100% 15N] PCP7T, 50 mM TRIS, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
uMPCP7T-1[U-100% 13C; U-100% 15N]350-5001
50 mMTRIS-21
500 uMPCP7T-32
50 mMTRIS-42
500 uMPCP7T-53
50 mMTRIS-63
uMPCP7T-7[U-100% 15N]350-5004
50 mMTRIS-84
Sample conditionsIonic strength: 0.1 / pH: 7.4 / Pressure: ambient / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Oxford OMEGAOxfordOMEGA6001
Oxford OMEGAOxfordOMEGA7502
Oxford OMEGAOxfordOMEGA9503

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Processing

NMR software
NameVersionDeveloperClassification
CcpNmr Analysis2.2CCPNchemical shift assignment
CcpNmr Analysis2.2CCPNpeak picking
YASARA1.1YASARA Biosciences GmbHprocessing
YASARA1.1YASARA Biosciences GmbHrefinement
YASARA1.1Cornilescu, Delaglio and Baxprocessing
YASARA1.1Cornilescu, Delaglio and Baxrefinement
YASARA1.1YASARA Biosciences GmbHprocessing
YASARA1.1YASARA Biosciences GmbHrefinement
YASARA1.1Cornilescu, Delaglio and Baxprocessing
YASARA1.1Cornilescu, Delaglio and Baxrefinement
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
WHAT IFVrienddata analysis
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 20 / Conformers submitted total number: 20

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