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- PDB-5w4j: X-ray crystallographic structure of a beta-hairpin peptide mimic.... -

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Basic information

Entry
Database: PDB / ID: 5w4j
TitleX-ray crystallographic structure of a beta-hairpin peptide mimic. (ORN)KLV(MEA)FAE(ORN)AIIGLMV.
ComponentsA-beta 17_36 peptide: ORN-LYS-VAL-PHE-MEA-ALA-ALA-ASP-ORN-ALA-ILE-ILE-GLY-LEU-MET-VAL
KeywordsDE NOVO PROTEIN / amyloid / oligomer / PROTEIN FIBRIL
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SAD / Resolution: 2.08 Å
AuthorsKreutzer, A.G. / 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: Biochemistry / Year: 2017
Title: A Hexamer of a Peptide Derived from A beta 16-36.
Authors: Kreutzer, A.G. / Spencer, R.K. / McKnelly, K.J. / Yoo, S. / Hamza, I.L. / Salveson, P.J. / Nowick, J.S.
History
DepositionJun 11, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 22, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Jan 1, 2020Group: Atomic model / Author supporting evidence / Category: atom_site / pdbx_audit_support
Item: _atom_site.occupancy / _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: A-beta 17_36 peptide: ORN-LYS-VAL-PHE-MEA-ALA-ALA-ASP-ORN-ALA-ILE-ILE-GLY-LEU-MET-VAL
B: A-beta 17_36 peptide: ORN-LYS-VAL-PHE-MEA-ALA-ALA-ASP-ORN-ALA-ILE-ILE-GLY-LEU-MET-VAL
C: A-beta 17_36 peptide: ORN-LYS-VAL-PHE-MEA-ALA-ALA-ASP-ORN-ALA-ILE-ILE-GLY-LEU-MET-VAL
D: A-beta 17_36 peptide: ORN-LYS-VAL-PHE-MEA-ALA-ALA-ASP-ORN-ALA-ILE-ILE-GLY-LEU-MET-VAL
E: A-beta 17_36 peptide: ORN-LYS-VAL-PHE-MEA-ALA-ALA-ASP-ORN-ALA-ILE-ILE-GLY-LEU-MET-VAL
F: A-beta 17_36 peptide: ORN-LYS-VAL-PHE-MEA-ALA-ALA-ASP-ORN-ALA-ILE-ILE-GLY-LEU-MET-VAL


Theoretical massNumber of molelcules
Total (without water)10,4296
Polymers10,4296
Non-polymers00
Water1,13563
1
A: A-beta 17_36 peptide: ORN-LYS-VAL-PHE-MEA-ALA-ALA-ASP-ORN-ALA-ILE-ILE-GLY-LEU-MET-VAL
D: A-beta 17_36 peptide: ORN-LYS-VAL-PHE-MEA-ALA-ALA-ASP-ORN-ALA-ILE-ILE-GLY-LEU-MET-VAL

A: A-beta 17_36 peptide: ORN-LYS-VAL-PHE-MEA-ALA-ALA-ASP-ORN-ALA-ILE-ILE-GLY-LEU-MET-VAL
D: A-beta 17_36 peptide: ORN-LYS-VAL-PHE-MEA-ALA-ALA-ASP-ORN-ALA-ILE-ILE-GLY-LEU-MET-VAL


Theoretical massNumber of molelcules
Total (without water)6,9534
Polymers6,9534
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556x,-y+1/2,-z+11
Buried area2490 Å2
ΔGint-24 kcal/mol
Surface area4140 Å2
MethodPISA
2
B: A-beta 17_36 peptide: ORN-LYS-VAL-PHE-MEA-ALA-ALA-ASP-ORN-ALA-ILE-ILE-GLY-LEU-MET-VAL
C: A-beta 17_36 peptide: ORN-LYS-VAL-PHE-MEA-ALA-ALA-ASP-ORN-ALA-ILE-ILE-GLY-LEU-MET-VAL
E: A-beta 17_36 peptide: ORN-LYS-VAL-PHE-MEA-ALA-ALA-ASP-ORN-ALA-ILE-ILE-GLY-LEU-MET-VAL
F: A-beta 17_36 peptide: ORN-LYS-VAL-PHE-MEA-ALA-ALA-ASP-ORN-ALA-ILE-ILE-GLY-LEU-MET-VAL


Theoretical massNumber of molelcules
Total (without water)6,9534
Polymers6,9534
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2430 Å2
ΔGint-24 kcal/mol
Surface area4230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)30.590, 46.939, 64.302
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number17
Space group name H-MP2212
Components on special symmetry positions
IDModelComponents
11A-116-

HOH

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Components

#1: Protein/peptide
A-beta 17_36 peptide: ORN-LYS-VAL-PHE-MEA-ALA-ALA-ASP-ORN-ALA-ILE-ILE-GLY-LEU-MET-VAL


Mass: 1738.165 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / Source method: isolated from a natural source / Formula: H2O

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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: 2.21 Å3/Da / Density % sol: 44.43 %
Crystal growTemperature: 296.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.05 M HEPES buffer (pH 7.5), 0.2 M KCl, 37% Pentaerythritol propoxylate (5/4 PO/OH)
PH range: 7.5-8.5

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Data collection

DiffractionMean temperature: 133 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 92 / Detector: CCD / Date: Feb 2, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.08→32.15 Å / Num. obs: 5952 / % possible obs: 99.82 % / Redundancy: 17.4 % / Rmerge(I) obs: 0.007097 / Net I/σ(I): 71.11
Reflection shellResolution: 2.08→2.154 Å / Redundancy: 12.6 % / Rmerge(I) obs: 0.01986 / Mean I/σ(I) obs: 28.06 / Num. unique obs: 581 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.08→32.15 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.42
RfactorNum. reflection% reflection
Rfree0.2431 1059 9.85 %
Rwork0.196 --
obs0.2007 5946 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.08→32.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms726 0 0 63 789
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007738
X-RAY DIFFRACTIONf_angle_d1.18972
X-RAY DIFFRACTIONf_dihedral_angle_d26.252480
X-RAY DIFFRACTIONf_chiral_restr0.138120
X-RAY DIFFRACTIONf_plane_restr0.005114
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.08-2.17470.29011320.21511199X-RAY DIFFRACTION100
2.1747-2.28930.26911360.20871208X-RAY DIFFRACTION100
2.2893-2.43280.28041380.22051216X-RAY DIFFRACTION100
2.4328-2.62050.2531300.22071191X-RAY DIFFRACTION100
2.6205-2.88420.26131330.22341214X-RAY DIFFRACTION100
2.8842-3.30130.22171360.20181219X-RAY DIFFRACTION100
3.3013-4.15850.21591270.17451219X-RAY DIFFRACTION100
4.1585-37.91880.24391270.1821222X-RAY DIFFRACTION99
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)
18.60318.66273.4329.45022.77862.1769-0.1137-0.063-0.2820.04240.1239-0.3232-0.3241-0.0338-0.03430.25890.05390.02040.15860.01110.169210.428617.477629.0567
22.41383.414-2.15278.8858-2.67566.37420.09420.08580.22830.23120.08950.0813-0.11840.3212-0.15730.1645-0.01570.0060.2526-0.00420.179312.442416.319314.0533
35.29865.1833.20495.63773.27332.00210.06150.84030.320.27820.33720.71190.2016-0.7570.05540.3556-0.0722-0.0440.31390.01320.22372.537914.424817.7835
47.4408-3.57332.03433.74170.32465.7104-0.2563-0.2487-0.93740.01390.32410.46961.0959-0.4498-0.35980.4782-0.15340.07230.32990.03340.3195.45647.593516.7366
56.7049-4.82011.91053.8138-2.71386.166-0.49680.00130.28140.42330.4599-0.0404-0.42490.5749-0.06730.3104-0.0047-0.00220.23840.00090.195413.546815.501939.273
68.06181-1.99998.77842.35695.41890.13140.17131.6572-0.012-0.61280.047-1.0124-0.73040.12730.42510.0904-0.01240.2475-0.09820.2546.118516.121638.1013
76.7032-3.98-0.32229.0674-3.40481.985-0.01370.04690.4060.6693-0.2257-0.9987-1.3335-0.54540.01730.29880.1410.00230.3981-0.12160.20399.984618.13923.4608
86.18870.37193.69078.3293-2.44516.28140.50550.7107-0.3684-0.701-0.3836-0.7942-0.18190.5401-0.16740.35350.02350.07380.3667-0.05380.32314.221612.42864.5424
98.64660.70842.31382.3495-2.95649.3207-0.21830.19420.1934-0.11980.16120.78540.2588-1.45740.28710.39-0.0271-0.0560.44430.03790.29043.125510.50546.473
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 8 )
4X-RAY DIFFRACTION4chain 'C' and (resid 9 through 16 )
5X-RAY DIFFRACTION5chain 'D' and (resid 1 through 8 )
6X-RAY DIFFRACTION6chain 'D' and (resid 9 through 16 )
7X-RAY DIFFRACTION7chain 'E' and (resid 1 through 8 )
8X-RAY DIFFRACTION8chain 'E' and (resid 9 through 16 )
9X-RAY DIFFRACTION9chain 'F' and (resid 1 through 16 )

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