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- PDB-5v63: Crystal structure of macrocycles containing Abeta 16-22 (KLV(PHI)... -

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Basic information

Entry
Database: PDB / ID: 5v63
TitleCrystal structure of macrocycles containing Abeta 16-22 (KLV(PHI)FAE) and Abeta 30-36 (AII(SAR)L(ORN)V)
ComponentsORN-LYS-LEU-VAL-PHI-PHE-ALA-GLU-ORN-ALA-ILE-ILE-SAR-LEU-MET-VAL
KeywordsDE NOVO PROTEIN / beta-hairpin / macrocycle
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SAD / Resolution: 2.091 Å
AuthorsSpencer, R.K. / Salveson, P.J. / 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
Revision 1.4Apr 2, 2025Group: 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.pdbx_dist_value / _struct_conn.ptnr1_label_atom_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

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Assembly

Deposited unit
A: ORN-LYS-LEU-VAL-PHI-PHE-ALA-GLU-ORN-ALA-ILE-ILE-SAR-LEU-MET-VAL


Theoretical massNumber of molelcules
Total (without water)2,0191
Polymers2,0191
Non-polymers00
Water1086
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: ORN-LYS-LEU-VAL-PHI-PHE-ALA-GLU-ORN-ALA-ILE-ILE-SAR-LEU-MET-VAL
x 12


Theoretical massNumber of molelcules
Total (without water)24,23212
Polymers24,23212
Non-polymers00
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation3_556-x,y,-z+11
crystal symmetry operation4_566x,-y+1,-z+11
crystal symmetry operation33_455y-1/2,z,x+1/21
crystal symmetry operation34_555-y+1/2,z,-x+1/21
crystal symmetry operation35_465y-1/2,-z+1,-x+1/21
crystal symmetry operation36_565-y+1/2,-z+1,x+1/21
crystal symmetry operation41_455z-1/2,x+1/2,y1
crystal symmetry operation42_456z-1/2,-x+1/2,-y+11
crystal symmetry operation43_555-z+1/2,-x+1/2,y1
crystal symmetry operation44_556-z+1/2,x+1/2,-y+11
Buried area10840 Å2
ΔGint-107 kcal/mol
Surface area9500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.010, 55.010, 55.010
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number196
Space group name H-MF23
Components on special symmetry positions
IDModelComponents
11A-104-

HOH

21A-106-

HOH

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Components

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


Mass: 2019.298 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 28.38 %
Crystal growTemperature: 296.15 K / Method: vapor diffusion, hanging drop / Details: 0.1 M HEPES, pH 7.0 0.2 M MgCl2 28% 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: May 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.091→19.449 Å / Num. obs: 1623 / % possible obs: 100 % / Redundancy: 2 % / Rmerge(I) obs: 0.027 / Net I/σ(I): 28.66
Reflection shellResolution: 2.091→2.166 Å / Redundancy: 2 % / Rmerge(I) obs: 0.077 / Mean I/σ(I) obs: 10.28 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.091→19.449 Å / Cross valid method: FREE R-VALUE / σ(F): 1.52 / Phase error: 30.19
RfactorNum. reflection% reflection
Rfree0.2694 174 10.72 %
Rwork0.2567 --
obs0.2762 1623 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.091→19.449 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms126 0 0 6 132
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005137
X-RAY DIFFRACTIONf_angle_d0.766184
X-RAY DIFFRACTIONf_dihedral_angle_d30.03591
X-RAY DIFFRACTIONf_chiral_restr0.05123
X-RAY DIFFRACTIONf_plane_restr0.00522
Refinement TLS params.Method: refined / Origin x: 9.4181 Å / Origin y: 17.8473 Å / Origin z: 27.5174 Å
111213212223313233
T0.1765 Å20.01 Å2-0.0485 Å2-0.2097 Å2-0.0163 Å2--0.1704 Å2
L9.5609 °27.8943 °2-8.1421 °2-8.6467 °2-7.4905 °2--7.4825 °2
S-0.0369 Å °0.1856 Å °0.5765 Å °-0.1538 Å °0.2147 Å °0.6616 Å °-0.1435 Å °-0.5483 Å °-0.2589 Å °
Refinement TLS groupSelection details: chain 'A' and (resid 1 through 16 )

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