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- PDB-5v65: Crystal structure of macrocycles containing Abeta 17-23 (LV(PHI)F... -

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Basic information

Entry
Database: PDB / ID: 5v65
TitleCrystal structure of macrocycles containing Abeta 17-23 (LV(PHI)FAED) and Abeta 30-36 (AII(SAR)L(ORN)V)
ComponentsORN-LEU-VAL-PHI-PHE-ALA-GLU-ASP-ORN-ALA-ILE-ILE-SAR-LEU-MET-VAL
KeywordsDE NOVO PROTEIN / beta-hairpin / macrocycle
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SAD / Resolution: 2.52 Å
AuthorsKreutzer, A.G. / 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 / Database references / Category: pdbx_audit_support / struct_ref_seq
Item: _pdbx_audit_support.funding_organization / _struct_ref_seq.db_align_end
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

Downloads & links

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Assembly

Deposited unit
A: ORN-LEU-VAL-PHI-PHE-ALA-GLU-ASP-ORN-ALA-ILE-ILE-SAR-LEU-MET-VAL
B: ORN-LEU-VAL-PHI-PHE-ALA-GLU-ASP-ORN-ALA-ILE-ILE-SAR-LEU-MET-VAL
C: ORN-LEU-VAL-PHI-PHE-ALA-GLU-ASP-ORN-ALA-ILE-ILE-SAR-LEU-MET-VAL
D: ORN-LEU-VAL-PHI-PHE-ALA-GLU-ASP-ORN-ALA-ILE-ILE-SAR-LEU-MET-VAL
E: ORN-LEU-VAL-PHI-PHE-ALA-GLU-ASP-ORN-ALA-ILE-ILE-SAR-LEU-MET-VAL
F: ORN-LEU-VAL-PHI-PHE-ALA-GLU-ASP-ORN-ALA-ILE-ILE-SAR-LEU-MET-VAL
G: ORN-LEU-VAL-PHI-PHE-ALA-GLU-ASP-ORN-ALA-ILE-ILE-SAR-LEU-MET-VAL
H: ORN-LEU-VAL-PHI-PHE-ALA-GLU-ASP-ORN-ALA-ILE-ILE-SAR-LEU-MET-VAL
I: ORN-LEU-VAL-PHI-PHE-ALA-GLU-ASP-ORN-ALA-ILE-ILE-SAR-LEU-MET-VAL
J: ORN-LEU-VAL-PHI-PHE-ALA-GLU-ASP-ORN-ALA-ILE-ILE-SAR-LEU-MET-VAL
K: ORN-LEU-VAL-PHI-PHE-ALA-GLU-ASP-ORN-ALA-ILE-ILE-SAR-LEU-MET-VAL
L: ORN-LEU-VAL-PHI-PHE-ALA-GLU-ASP-ORN-ALA-ILE-ILE-SAR-LEU-MET-VAL
M: ORN-LEU-VAL-PHI-PHE-ALA-GLU-ASP-ORN-ALA-ILE-ILE-SAR-LEU-MET-VAL
N: ORN-LEU-VAL-PHI-PHE-ALA-GLU-ASP-ORN-ALA-ILE-ILE-SAR-LEU-MET-VAL
O: ORN-LEU-VAL-PHI-PHE-ALA-GLU-ASP-ORN-ALA-ILE-ILE-SAR-LEU-MET-VAL
P: ORN-LEU-VAL-PHI-PHE-ALA-GLU-ASP-ORN-ALA-ILE-ILE-SAR-LEU-MET-VAL


Theoretical massNumber of molelcules
Total (without water)30,49716
Polymers30,49716
Non-polymers00
Water1,26170
1
A: ORN-LEU-VAL-PHI-PHE-ALA-GLU-ASP-ORN-ALA-ILE-ILE-SAR-LEU-MET-VAL


Theoretical massNumber of molelcules
Total (without water)1,9061
Polymers1,9061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ORN-LEU-VAL-PHI-PHE-ALA-GLU-ASP-ORN-ALA-ILE-ILE-SAR-LEU-MET-VAL


Theoretical massNumber of molelcules
Total (without water)1,9061
Polymers1,9061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: ORN-LEU-VAL-PHI-PHE-ALA-GLU-ASP-ORN-ALA-ILE-ILE-SAR-LEU-MET-VAL


Theoretical massNumber of molelcules
Total (without water)1,9061
Polymers1,9061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: ORN-LEU-VAL-PHI-PHE-ALA-GLU-ASP-ORN-ALA-ILE-ILE-SAR-LEU-MET-VAL


Theoretical massNumber of molelcules
Total (without water)1,9061
Polymers1,9061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: ORN-LEU-VAL-PHI-PHE-ALA-GLU-ASP-ORN-ALA-ILE-ILE-SAR-LEU-MET-VAL


Theoretical massNumber of molelcules
Total (without water)1,9061
Polymers1,9061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: ORN-LEU-VAL-PHI-PHE-ALA-GLU-ASP-ORN-ALA-ILE-ILE-SAR-LEU-MET-VAL


Theoretical massNumber of molelcules
Total (without water)1,9061
Polymers1,9061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: ORN-LEU-VAL-PHI-PHE-ALA-GLU-ASP-ORN-ALA-ILE-ILE-SAR-LEU-MET-VAL


Theoretical massNumber of molelcules
Total (without water)1,9061
Polymers1,9061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: ORN-LEU-VAL-PHI-PHE-ALA-GLU-ASP-ORN-ALA-ILE-ILE-SAR-LEU-MET-VAL


Theoretical massNumber of molelcules
Total (without water)1,9061
Polymers1,9061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
I: ORN-LEU-VAL-PHI-PHE-ALA-GLU-ASP-ORN-ALA-ILE-ILE-SAR-LEU-MET-VAL


Theoretical massNumber of molelcules
Total (without water)1,9061
Polymers1,9061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
10
J: ORN-LEU-VAL-PHI-PHE-ALA-GLU-ASP-ORN-ALA-ILE-ILE-SAR-LEU-MET-VAL


Theoretical massNumber of molelcules
Total (without water)1,9061
Polymers1,9061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
11
K: ORN-LEU-VAL-PHI-PHE-ALA-GLU-ASP-ORN-ALA-ILE-ILE-SAR-LEU-MET-VAL


Theoretical massNumber of molelcules
Total (without water)1,9061
Polymers1,9061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
12
L: ORN-LEU-VAL-PHI-PHE-ALA-GLU-ASP-ORN-ALA-ILE-ILE-SAR-LEU-MET-VAL


Theoretical massNumber of molelcules
Total (without water)1,9061
Polymers1,9061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
13
M: ORN-LEU-VAL-PHI-PHE-ALA-GLU-ASP-ORN-ALA-ILE-ILE-SAR-LEU-MET-VAL


Theoretical massNumber of molelcules
Total (without water)1,9061
Polymers1,9061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
14
N: ORN-LEU-VAL-PHI-PHE-ALA-GLU-ASP-ORN-ALA-ILE-ILE-SAR-LEU-MET-VAL


Theoretical massNumber of molelcules
Total (without water)1,9061
Polymers1,9061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
15
O: ORN-LEU-VAL-PHI-PHE-ALA-GLU-ASP-ORN-ALA-ILE-ILE-SAR-LEU-MET-VAL


Theoretical massNumber of molelcules
Total (without water)1,9061
Polymers1,9061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
16
P: ORN-LEU-VAL-PHI-PHE-ALA-GLU-ASP-ORN-ALA-ILE-ILE-SAR-LEU-MET-VAL


Theoretical massNumber of molelcules
Total (without water)1,9061
Polymers1,9061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.719, 67.719, 169.612
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

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


Mass: 1906.075 Da / Num. of mol.: 16 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / 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: 2.45 Å3/Da / Density % sol: 49.72 %
Crystal growTemperature: 296.15 K / Method: vapor diffusion, hanging drop / Details: 0.1 M HEPES, pH 6 24% Jeffamine

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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: Jun 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.52→33.86 Å / Num. obs: 9726 / % possible obs: 98.84 % / Redundancy: 12.7 % / Rmerge(I) obs: 0.6832 / Net I/σ(I): 240.79
Reflection shellResolution: 2.52→2.61 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.6704 / Mean I/σ(I) obs: 25.2 / Num. unique obs: 906 / % possible all: 98.84

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.52→33.86 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 2.02 / Phase error: 33.58
RfactorNum. reflection% reflection
Rfree0.281 1825 9.83 %
Rwork0.222 --
obs0.228 18572 94.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.52→33.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1895 0 105 70 2070
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042032
X-RAY DIFFRACTIONf_angle_d0.9152720
X-RAY DIFFRACTIONf_dihedral_angle_d25.2461344
X-RAY DIFFRACTIONf_chiral_restr0.095336
X-RAY DIFFRACTIONf_plane_restr0.005336
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.52-2.58810.30271380.3021095X-RAY DIFFRACTION84
2.5881-2.66420.35031110.3271202X-RAY DIFFRACTION87
2.6642-2.75020.41221350.30481287X-RAY DIFFRACTION92
2.7502-2.84850.39821380.28341255X-RAY DIFFRACTION93
2.8485-2.96240.32651540.26241230X-RAY DIFFRACTION93
2.9624-3.09720.37911330.24381335X-RAY DIFFRACTION95
3.0972-3.26040.35451430.27571284X-RAY DIFFRACTION95
3.2604-3.46450.39781490.24561318X-RAY DIFFRACTION98
3.4645-3.73170.27081310.2321348X-RAY DIFFRACTION99
3.7317-4.10660.24841510.17881334X-RAY DIFFRACTION99
4.1066-4.69960.18461400.16141368X-RAY DIFFRACTION99
4.6996-5.91610.18251460.16841350X-RAY DIFFRACTION99
5.9161-34.36530.27221560.20981341X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
19.4649-4.2718-2.41377.9632-4.06535.01780.3150.4981-0.0240.58170.3059-0.5444-0.13380.2961-0.46090.3157-0.1112-0.00150.3601-0.03110.413625.286746.7895101.2779
22.3913-0.4659-0.50565.9649-3.5947.8233-0.2125-0.43590.7941-0.7668-0.3639-0.4209-0.21030.5740.19120.2398-0.0505-0.04170.29720.09670.398719.120356.6429103.0368
35.92432.0715-4.87354.73132.79949.0730.659-0.45160.0167-0.13740.3849-0.0754-0.4030.6277-0.21360.3453-0.0439-0.11170.35720.03430.455624.243854.518492.8635
46.78990.785-3.02338.415-2.40911.8552-0.38270.83070.5525-0.3877-0.2232-0.3637-0.0392-0.62610.30020.25730.0537-0.07010.4170.01040.290214.717239.915291.106
55.331-4.4636-0.60095.3986-2.5877.85740.4516-0.2382-0.11690.2467-0.9910.12250.0142-0.42990.38540.331-0.0869-0.03610.3469-0.0150.25078.31645.020199.333
65.2062-2.88461.67933.07341.11353.9239-0.2139-0.13780.1765-0.2443-0.45030.57480.1820.15210.58290.3039-0.05230.01890.3813-0.00650.41389.849450.140989.2752
76.60530.5368-2.85358.5399-2.63479.112-0.6332-0.0018-0.1537-0.0570.2225-0.2362-0.8694-0.03140.28350.4795-0.0072-0.05940.5227-0.01750.2087-0.921245.679275.7009
88.0551.2576-0.40164.44373.49094.48920.1530.0192-0.3511-1.49220.025-0.3648-0.6194-0.95340.17430.6282-0.0502-0.10750.3688-0.03450.3461-5.057643.424860.3086
95.6757-0.8393-1.01614.83322.34434.4630.1298-0.54890.9367-0.4003-0.4426-0.9256-1.05-0.14710.36260.39470.0057-0.10260.24770.01190.42355.653964.4015110.7084
106.6816-2.60572.34877.61483.60595.2814-0.12650.4608-0.0421-0.2050.35070.0131-0.671-0.1246-0.29570.4308-0.06290.08410.16130.04390.3776-5.969664.8581112.4235
116.29831.6943-3.62658.08732.62943.79090.48110.30950.3357-0.250.16410.31760.00730.1155-0.6880.43820.0507-0.0320.29680.0410.32851.213167.8049120.8366
125.34143.0093-1.99536.3223-3.89834.2569-0.20510.0224-0.0541-0.3999-0.31580.2132-0.5485-0.04450.13860.3360.0332-0.10460.1542-0.05140.324.607553.1721124.3969
135.5551.2585-0.48744.13381.01523.88830.0812-0.22140.01910.3022-0.1157-0.25910.54120.234-0.88320.48550.1101-0.09240.30510.05260.1807-6.639552.2341122.5589
148.4597-3.752.89239.20194.36435.583-0.2848-0.4108-0.0886-0.2087-0.1508-0.20620.05530.06790.29890.3115-0.021-0.03750.21320.10150.23760.986449.2348114.3605
159.3459-2.456-3.9039.1602-3.97224.64730.0545-0.2878-0.2635-0.5917-0.30790.1933-0.3103-0.79850.28820.52290.0420.02340.4807-0.08320.2024-5.239243.1914138.0042
165.51330.2976-0.85434.12020.94434.53260.5547-0.52410.01290.5909-0.3130.58460.57570.42510.24730.4059-0.11840.00590.50740.06760.25596.272536.8913153.4032
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 16 )
2X-RAY DIFFRACTION2chain 'B' and (resid 1 through 16 )
3X-RAY DIFFRACTION3chain 'C' and (resid 1 through 16 )
4X-RAY DIFFRACTION4chain 'D' and (resid 1 through 16 )
5X-RAY DIFFRACTION5chain 'E' and (resid 1 through 16 )
6X-RAY DIFFRACTION6chain 'F' and (resid 1 through 16 )
7X-RAY DIFFRACTION7chain 'G' and (resid 1 through 16 )
8X-RAY DIFFRACTION8chain 'H' and (resid 1 through 16 )
9X-RAY DIFFRACTION9chain 'I' and (resid 1 through 16 )
10X-RAY DIFFRACTION10chain 'J' and (resid 1 through 16 )
11X-RAY DIFFRACTION11chain 'K' and (resid 1 through 16 )
12X-RAY DIFFRACTION12chain 'L' and (resid 1 through 16 )
13X-RAY DIFFRACTION13chain 'M' and (resid 1 through 16 )
14X-RAY DIFFRACTION14chain 'N' and (resid 1 through 16 )
15X-RAY DIFFRACTION15chain 'O' and (resid 1 through 16 )
16X-RAY DIFFRACTION16chain 'P' and resid ' 5 ' and name ' I ' and altloc ' '

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