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- PDB-5v64: Crystal structure of macrocycles containing Abeta 15-21 (QKLV(PHI... -

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Basic information

Entry
Database: PDB / ID: 5v64
TitleCrystal structure of macrocycles containing Abeta 15-21 (QKLV(PHI)FA) and Abeta 30-36 (AII(SAR)L(ORN)V)
ComponentsORN-GLN-LYS-LEU-VAL-PHI-PHE-ALA-ORN-ALA-ILE-ILE-SAR-LEU-MET-VAL
KeywordsDE NOVO PROTEIN / beta-hairpin / macrocycle
Function / homologyCITRATE ANION
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SAD / Resolution: 2.023 Å
AuthorsSalveson, P.J. / Spencer, R.K. / Nowick, J.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM097562 United States
CitationJournal: Org. Lett. / Year: 2017
Title: X-ray Crystallographic Structure of a Compact Dodecamer from a Peptide Derived from A beta 16-36.
Authors: Salveson, P.J. / Spencer, R.K. / Kreutzer, A.G. / Nowick, J.S.
History
DepositionMar 15, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 28, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 5, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jul 26, 2017Group: Advisory / Author supporting evidence / Database references
Category: citation / citation_author ...citation / citation_author / pdbx_audit_support / pdbx_validate_polymer_linkage
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 / _pdbx_audit_support.funding_organization
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ORN-GLN-LYS-LEU-VAL-PHI-PHE-ALA-ORN-ALA-ILE-ILE-SAR-LEU-MET-VAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,1544
Polymers1,9191
Non-polymers2353
Water1629
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area370 Å2
ΔGint-13 kcal/mol
Surface area1840 Å2
2
A: ORN-GLN-LYS-LEU-VAL-PHI-PHE-ALA-ORN-ALA-ILE-ILE-SAR-LEU-MET-VAL
hetero molecules

A: ORN-GLN-LYS-LEU-VAL-PHI-PHE-ALA-ORN-ALA-ILE-ILE-SAR-LEU-MET-VAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,3098
Polymers3,8382
Non-polymers4706
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area1150 Å2
ΔGint-29 kcal/mol
Surface area3160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)20.346, 22.029, 31.598
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-102-

NA

21A-206-

HOH

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Components

#1: Protein/peptide ORN-GLN-LYS-LEU-VAL-PHI-PHE-ALA-ORN-ALA-ILE-ILE-SAR-LEU-MET-VAL


Mass: 1919.182 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O
Compound detailschemical models of beta-amyloid oligomerization. They are designed to mimic a beta-hairpin formed ...chemical models of beta-amyloid oligomerization. They are designed to mimic a beta-hairpin formed by beta-amyloid, that is thought to self-assemble giving rise to neurotoxic oligomers of beta-amyloid in Alzheimer's diseased brains

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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: 1.84 Å3/Da / Density % sol: 33.33 %
Crystal growTemperature: 296.15 K / Method: vapor diffusion, hanging drop
Details: 0.1 M sodium citrate, pH 5.25 24% PEG 4000 23% isopropanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Jul 31, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.023→18.07 Å / Num. obs: 4263 / % possible obs: 97.84 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.1042 / Net I/σ(I): 14.02
Reflection shellResolution: 2.023→2.095 Å / Rmerge(I) obs: 0.2209 / Mean I/σ(I) obs: 4.69 / Num. unique obs: 204 / % possible all: 85.29

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.023→18.07 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.58
RfactorNum. reflection% reflection
Rfree0.2441 170 10.07 %
Rwork0.195 --
obs0.2003 1689 93.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.023→18.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms126 0 15 9 150
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005140
X-RAY DIFFRACTIONf_angle_d1.145187
X-RAY DIFFRACTIONf_dihedral_angle_d30.94164
X-RAY DIFFRACTIONf_chiral_restr0.04421
X-RAY DIFFRACTIONf_plane_restr0.00623
Refinement TLS params.Method: refined / Origin x: 5.7013 Å / Origin y: 13.3747 Å / Origin z: 11.1603 Å
111213212223313233
T0.14 Å20.0157 Å20.0251 Å2-0.1363 Å20.0014 Å2--0.1524 Å2
L3.8225 °20.5004 °21.4037 °2-4.2247 °22.6566 °2--2.1791 °2
S0.1107 Å °0.3609 Å °-0.0183 Å °-0.1779 Å °-0.0886 Å °-0.1583 Å °-0.0531 Å °-0.0781 Å °0.0738 Å °
Refinement TLS groupSelection details: chain 'A' and (resid 1 through 16 )

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