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- PDB-6dky: Crystal structure of ribifolin, an orbitide from Jatropha ribifolia -

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Basic information

Entry
Database: PDB / ID: 6dky
TitleCrystal structure of ribifolin, an orbitide from Jatropha ribifolia
ComponentsILE-LEU-GLY-SER-ILE-ILE-LEU-GLY
KeywordsUNKNOWN FUNCTION / cyclic peptide
Biological speciesJatropha (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.239 Å
AuthorsWang, C.K. / Ramalho, S.D. / King, G.J. / Craik, D.J.
Funding support Brazil, Australia, 2items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)#2016/13148-4 Brazil
Australian Research Council (ARC)FL150100146 Australia
CitationJournal: J. Nat. Prod. / Year: 2018
Title: Synthesis, Racemic X-ray Crystallographic, and Permeability Studies of Bioactive Orbitides from Jatropha Species.
Authors: Ramalho, S.D. / Wang, C.K. / King, G.J. / Byriel, K.A. / Huang, Y.H. / Bolzani, V.S. / Craik, D.J.
History
DepositionMay 31, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 7, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 5, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / struct_conn
Item: _pdbx_audit_support.funding_organization / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ILE-LEU-GLY-SER-ILE-ILE-LEU-GLY
B: ILE-LEU-GLY-SER-ILE-ILE-LEU-GLY


Theoretical massNumber of molelcules
Total (without water)1,5702
Polymers1,5702
Non-polymers00
Water362
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area250 Å2
ΔGint-2 kcal/mol
Surface area1580 Å2
Unit cell
Length a, b, c (Å)19.142, 23.632, 23.851
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein/peptide ILE-LEU-GLY-SER-ILE-ILE-LEU-GLY


Mass: 784.986 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Jatropha (plant)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.72 Å3/Da / Density % sol: 28.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1 M Tris base (pH 8.0) and 40% 2-methyl-2,4-pentanediol (MPD)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 26, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.239→16.79 Å / Num. obs: 3333 / % possible obs: 99.9 % / Redundancy: 11.9 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 18.4
Reflection shellResolution: 1.239→1.284 Å / Rmerge(I) obs: 0.224 / Num. unique all: 292

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Processing

Software
NameVersionClassification
PHENIX(1.10_2142: ???)refinement
XDSdata reduction
XDSdata scaling
SHELXCDphasing
RefinementResolution: 1.239→16.79 Å / SU ML: 0.08 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 25.09
RfactorNum. reflection% reflection
Rfree0.2226 336 10.1 %
Rwork0.1964 --
obs0.1992 3327 99.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.239→16.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms108 0 0 2 110
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.019108
X-RAY DIFFRACTIONf_angle_d1.689140
X-RAY DIFFRACTIONf_dihedral_angle_d7.44536
X-RAY DIFFRACTIONf_chiral_restr0.13222
X-RAY DIFFRACTIONf_plane_restr0.00814
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2393-1.56130.2251660.19211445X-RAY DIFFRACTION99
1.5613-19.14430.22171700.1981546X-RAY DIFFRACTION100

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