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- PDB-8v4b: NMR structure of a synthetic analogue of Ramoplanin A2 -

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Basic information

Entry
Database: PDB / ID: 8v4b
TitleNMR structure of a synthetic analogue of Ramoplanin A2
ComponentsRamoplanin A2 synthetic analogue
KeywordsANTIBIOTIC / Antibiotic peptide / Synthetic peptide / Ramoplanin A2 / non ribosomal peptide / arylglycine / solid phase peptide synthesis
Function / homologyHEXANOIC ACID
Function and homology information
Biological speciesActinoplanes (bacteria)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsSwarbrick, J.D. / Marschall, E.A. / Cryle, M.J. / Tailhades, J.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)2003325 Australia
CitationJournal: Chem Sci / Year: 2023
Title: Synthetic ramoplanin analogues are accessible by effective incorporation of arylglycines in solid-phase peptide synthesis.
Authors: Marschall, E. / Cass, R.W. / Prasad, K.M. / Swarbrick, J.D. / McKay, A.I. / Payne, J.A.E. / Cryle, M.J. / Tailhades, J.
History
DepositionNov 28, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 16, 2025Provider: repository / Type: Initial release
Revision 2.0Apr 23, 2025Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / entity ...atom_site / entity / entity_poly / entity_poly_seq / pdbx_entity_nonpoly / pdbx_entity_src_syn / pdbx_modification_feature / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_struct_sheet_hbond / pdbx_validate_torsion / struct_asym / struct_conn / struct_ref_seq / struct_sheet_range
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.type_symbol / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_entity_src_syn.pdbx_end_seq_num / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq.db_align_beg / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.seq_align_end / _struct_sheet_range.beg_auth_comp_id / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.beg_label_comp_id / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_auth_comp_id / _struct_sheet_range.end_auth_seq_id / _struct_sheet_range.end_label_comp_id / _struct_sheet_range.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Ramoplanin A2 synthetic analogue
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,1492
Polymers2,0331
Non-polymers1161
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR Distance Restraints, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200target function
RepresentativeModel #1fewest violations

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Components

#1: Protein/peptide Ramoplanin A2 synthetic analogue


Mass: 2033.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Actinoplanes (bacteria)
#2: Chemical ChemComp-6NA / HEXANOIC ACID


Mass: 116.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O2
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-1H NOESY 250-450ms
161isotropic12D 1H-1H NOESY 250-350ms
381isotropic12D 1H-1H NOESY 250-350ms
121isotropic12D 1H-1H TOCSY 70ms
271isotropic12D 1H-1H TOCSY 70ms
391isotropic12D 1H-1H TOCSY 70ms
131isotropic12D 1H-13C HSQC
141isotropic12D 13C H2BC
151isotropic12D 13C HMBC

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Sample preparation

DetailsType: solution
Contents: 4 mM Peptide, 10 mM D3 Acetate buffer, 80% H2O / 20% DMSO(D6)
Details: 4mM peptide/sa/sample. Recorded at 15C, 25C, and 40C
Label: all temps / Solvent system: 80% H2O / 20% DMSO(D6)
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
4 mMPeptidenatural abundance1
10 mMAcetate bufferD31
Sample conditions
Conditions-IDDetailsIonic strengthLabelpHPressure (kPa)Temperature (K)
180% H2O / 20% DMSO(D6) / 10mM Acetate pH 4.510 mM40C4.51 atm313 K
280% H2O / 20% DMSO(D6) / 10mM Acetate pH 4.510 mM25C4.51 atm298 K
380% H2O / 20% DMSO(D6) / 10mM Acetate pH 4.510 mM15C4.51 atm288 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Bruker AVANCEBrukerAVANCE6001Z axis cryoprobe
Bruker AVANCEBrukerAVANCE6002Z axis cryoprobe

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Processing

NMR software
NameVersionDeveloperClassification
CYANA3.97Guntert, Mumenthaler and Wuthrichrefinement
XEASYBartels et al.chemical shift assignment
NMRFAM-SPARKYLee W, Tonelli M, Markley JLchemical shift assignment
XEASYBartels et al.peak picking
CYANA3.97Guntert, Mumenthaler and Wuthrichstructure calculation
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 200 / Conformers submitted total number: 20

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