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- PDB-6vc1: Octreotide oxalate -

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Basic information

Entry
Database: PDB / ID: 6vc1
TitleOctreotide oxalate
ComponentsOctreotide
KeywordsDE NOVO PROTEIN / octreotide / somatostatin-14 analogue
Function / homologyOXALATE ION
Function and homology information
Biological speciesunidentified (others)
MethodPOWDER DIFFRACTION / SYNCHROTRON
AuthorsSpiliopoulou, M. / Karavassili, F. / Triandafillidis, D. / Valmas, A. / Kosinas, C. / Fili, S. / Barlos, K. / Barlos, K.K. / Morin, M. / Reinle-Schmitt, M. ...Spiliopoulou, M. / Karavassili, F. / Triandafillidis, D. / Valmas, A. / Kosinas, C. / Fili, S. / Barlos, K. / Barlos, K.K. / Morin, M. / Reinle-Schmitt, M. / Gozzo, F. / Margiolaki, I.
Funding support Greece, 2items
OrganizationGrant numberCountry
Hellenic Foundation for Research and Innovation (HFRI)3051 Greece
General Secretariat for Research and Technology (GSRT) Greece
CitationJournal: Acta Crystallogr.,Sect.A / Year: 2021
Title: New perspectives in macromolecular powder diffraction using single-photon-counting strip detectors: high-resolution structure of the pharmaceutical peptide octreotide.
Authors: Spiliopoulou, M. / Karavassili, F. / Triandafillidis, D.P. / Valmas, A. / Fili, S. / Kosinas, C. / Barlos, K. / Barlos, K.K. / Morin, M. / Reinle-Schmitt, M.L. / Gozzo, F. / Margiolaki, I.
History
DepositionDec 20, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2020Provider: repository / Type: Initial release
Revision 1.1May 19, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Remark 250 REFINEMENT. PROGRAM : GSAS AUTHORS : LARSON & VON DREELE DATA USED IN REFINEMENT RESOLUTION RANGE ... REFINEMENT. PROGRAM : GSAS AUTHORS : LARSON & VON DREELE DATA USED IN REFINEMENT RESOLUTION RANGE HIGH (ANGSTROMS) : 1.87 RESOLUTION RANGE LOW (ANGSTROMS) : 74.45 POWDER DIFFRACTION DATA. FIT TO DATA USED IN REFINEMENT NUMBER OF POWDER PATTERNS : 2 PROFILE R VALUES (%) : 6.29 5.61 WEIGHTED PROFILE R VALUES (%) : 8.44 7.40 F**2 R VALUES (%) : 45.95 43.29 NUMBERS OF POWDER PATTERN POINTS : 30815 29392 NUMBERS OF REFLECTIONS : 4926 4876 TOTAL NUMBER OF POWDER POINTS : 60207 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. PROTEIN ATOMS : NUCLEIC ACID ATOMS : HETEROGEN ATOMS : SOLVENT ATOMS : MODEL REFINEMENT. NUMBER OF LEAST-SQUARES PARAMETERS : 48 NUMBER OF RESTRAINTS : 968 LEAST-SQUARES MATRIX BAND WIDTH : 48 MARQUARDT COEFFICIENT : 8.49 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. NUMBER. INTERATOMIC DISTANCES (A) :0.014 300 BOND ANGLES (DEG) : 1.61 375 DISTANCES FROM RESTRAINT PLANES (A) :0.015 108 TORSION ANGLE RESTRAINTS (E) : 0.53 45 CHIRAL VOLUMES (A**3) :0.106 30 TORSION PSEUDOPOTENTIAL RESTRAINTS (E) : 4.22 23 ANTI-BUMPING DISTANCE RESTRAINTS (A) :0.029 50 HYDROGEN BOND DISTANCE RESTRAINTS (A) :0.345 37

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Octreotide
B: Octreotide
C: Octreotide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,1974
Polymers3,1093
Non-polymers881
Water55831
1
A: Octreotide
hetero molecules


  • defined by author
  • 1.12 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)1,1242
Polymers1,0361
Non-polymers881
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Octreotide


Theoretical massNumber of molelcules
Total (without water)1,0361
Polymers1,0361
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Octreotide


Theoretical massNumber of molelcules
Total (without water)1,0361
Polymers1,0361
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein/peptide Octreotide /


Mass: 1036.246 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) unidentified (others)
#2: Chemical ChemComp-OXL / OXALATE ION / Oxalate


Mass: 88.019 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2O4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: POWDER DIFFRACTION / Number of used crystals: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
11.8232.5
21.8232.5
Crystal grow
Temperature (K)Crystal-IDMethodDetails
2981evaporation, recrystallization0.2 M oxalic acid 434 mg mL-1 octreotide acetate 322.8 K until almost complete evaporation Redesolution in ddH2O 298 K until almost complete evaporation Repeat until crystal formation
2982evaporation, recrystallization0.2 M oxalic acid 500 mg mL-1 octreotide acetate 322.8 K until almost complete evaporation Redesolution in ddH2O 298 K until almost complete evaporation Repeat until crystal formation

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Type: SLS BEAMLINE X04SA / Wavelength: 1.3004392 Å
DetectorType: MYTHEN II Silicon Solid State 1D detector system / Detector: PIXEL / Date: Sep 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3004392 Å / Relative weight: 1

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Processing

SoftwareName: GSAS / Classification: refinement / Contact author: A.C. Larson, R.B. Von Dreele / Date: 2014 / Description: General Structure Analysis System

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