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- PDB-1jjz: REFINED STRUCTURE AND DISULFIDE PAIRING OF THE KALATA B1 PEPTIDE -

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Basic information

Entry
Database: PDB / ID: 1jjz
TitleREFINED STRUCTURE AND DISULFIDE PAIRING OF THE KALATA B1 PEPTIDE
ComponentsKalata-B4
KeywordsPLANT PROTEIN / cyclic peptide / cyclotide / disulfide pairing / uterotonic
Function / homology
Function and homology information


defense response / killing of cells of another organism / defense response to bacterium
Similarity search - Function
Cyclotide, moebius, conserved site / Cyclotides Moebius subfamily signature. / Cyclotides profile. / Cyclotide / Cyclotide superfamily / Cyclotide family
Similarity search - Domain/homology
KALATA B1 / Kalata-B1 / Kalata-B4
Similarity search - Component
Biological speciesOldenlandia affinis (plant)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsSkjeldal, L. / Gran, L. / Sletten, K. / Volkman, B.F.
Citation
Journal: Arch.Biochem.Biophys. / Year: 2002
Title: Refined structure and metal binding site of the kalata B1 peptide.
Authors: Skjeldal, L. / Gran, L. / Sletten, K. / Volkman, B.F.
#1: Journal: Biochemistry / Year: 1995
Title: Elucidation of the Primary and Three-Dimensional Structure of the Uterotonic Polypeptide Kalata B1
Authors: Saether, O. / Craik, D.J. / Campbell, I.D. / Sletten, K. / Juul, J. / Norman, D.G.
History
DepositionJul 10, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Aug 12, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: atom_site / entity ...atom_site / entity / entity_src_nat / pdbx_molecule_features / pdbx_nmr_software / pdbx_poly_seq_scheme / pdbx_struct_assembly / pdbx_struct_oper_list / pdbx_validate_close_contact / pdbx_validate_torsion / struct_conn / struct_mon_prot_cis / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _entity.pdbx_description / _entity_src_nat.pdbx_beg_seq_num / _entity_src_nat.pdbx_end_seq_num / _pdbx_nmr_software.name / _pdbx_poly_seq_scheme.pdb_seq_num / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _pdbx_validate_torsion.auth_seq_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_mon_prot_cis.auth_seq_id / _struct_mon_prot_cis.pdbx_auth_seq_id_2 / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Kalata-B4


Theoretical massNumber of molelcules
Total (without water)2,9171
Polymers2,9171
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50target function
Representative

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Components

#1: Protein/peptide Kalata-B4


Type: Cyclic peptide / Class: Antimicrobial, Antitumor / Mass: 2917.345 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: extracted from plant / Source: (natural) Oldenlandia affinis (plant)
References: UniProt: P83938, KALATA B1, UniProt: P56254*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 2D NOESY
NMR detailsText: Structure was determined using NOEs from a single 100 ms mixing time NOESY experiment

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Sample preparation

DetailsContents: 5 mM kalata B1; 90% H2O, 10% D2O / Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 0 / pH: 3 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 750 MHz

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Processing

NMR software
NameVersionDeveloperClassification
DYANA1.5P. Guentertrefinement
XwinNMR2.6Brukercollection
XEASY1.3.11C. Bartelsdata analysis
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: Structures are based on a total of 333 distance constraints. This includes 6 upper and 6 lower limits defining 3 disulfide bonds, as well as 3 upper and 3 lower limits defining a peptide ...Details: Structures are based on a total of 333 distance constraints. This includes 6 upper and 6 lower limits defining 3 disulfide bonds, as well as 3 upper and 3 lower limits defining a peptide bond cyclizing the peptide backbone. Residue numbering follows the original description of citation 1, except that for the purposes of structure calculations, the N-terminal residue was taken as Asn8. Therefore, residues 30-36 in this deposition correspond to residues 1-7 in citation 1 and related PDB entry 1kal. Structures were refined in the absence of any artificial constraints defining disulfide bonds until all NOEs had been assigned and low target functions were achieved (tf=0.6). 15 additional calculations were performed with these input data and the inclusion of constraints defining all possible disulfide pairing combinations. The structures containing disulfides between [5(34)-13], [17-29] and [22-27] displayed the lowest target function (0.74, second lowest was 1.54). On the basis of this result and analysis of NOEs observed between Cys sidechain protons, this disulfide bonding arrangement was assumed to be correct and served as the basis for this deposition.
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 50 / Conformers submitted total number: 20

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