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- PDB-5w4i: X-ray crystallographic structure of a beta-hairpin peptide mimic ... -

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Basic information

Entry
Database: PDB / ID: 5w4i
TitleX-ray crystallographic structure of a beta-hairpin peptide mimic derived from Abeta 16-36. Rigaku data set. (ORN)KLV(MEA)FAE(ORN)AIIGLMV.
ComponentsA-beta 17_36: ORN-LYS-LEU-VAL-MEA-PHE-ALA-GLU-ORN-ALA-ILE-ILE-GLY-LEU-MET-VAL
KeywordsDE NOVO PROTEIN / amyloid / oligomer / Alzheimer's / trimer / PROTEIN FIBRIL
Function / homologyIODIDE ION
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SAD / Resolution: 2.026 Å
AuthorsKreutzer, A.G. / McKnelly, K.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: 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 1.2Jan 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: A-beta 17_36: ORN-LYS-LEU-VAL-MEA-PHE-ALA-GLU-ORN-ALA-ILE-ILE-GLY-LEU-MET-VAL
B: A-beta 17_36: ORN-LYS-LEU-VAL-MEA-PHE-ALA-GLU-ORN-ALA-ILE-ILE-GLY-LEU-MET-VAL
C: A-beta 17_36: ORN-LYS-LEU-VAL-MEA-PHE-ALA-GLU-ORN-ALA-ILE-ILE-GLY-LEU-MET-VAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,12411
Polymers5,3833
Non-polymers7418
Water57632
1
A: A-beta 17_36: ORN-LYS-LEU-VAL-MEA-PHE-ALA-GLU-ORN-ALA-ILE-ILE-GLY-LEU-MET-VAL
B: A-beta 17_36: ORN-LYS-LEU-VAL-MEA-PHE-ALA-GLU-ORN-ALA-ILE-ILE-GLY-LEU-MET-VAL
C: A-beta 17_36: ORN-LYS-LEU-VAL-MEA-PHE-ALA-GLU-ORN-ALA-ILE-ILE-GLY-LEU-MET-VAL
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)48,99088
Polymers43,06324
Non-polymers5,92764
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_655-x+1,y,-z1
crystal symmetry operation4_555x,-y,-z1
crystal symmetry operation17_555x,z,-y1
crystal symmetry operation18_655-x+1,z,y1
crystal symmetry operation19_655-x+1,-z,-y1
crystal symmetry operation20_555x,-z,y1
Buried area27580 Å2
ΔGint-348 kcal/mol
Surface area18890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.746, 67.746, 67.746
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number207
Space group name H-MP432
Components on special symmetry positions
IDModelComponents
11A-103-

IOD

21B-102-

IOD

31A-208-

HOH

41A-209-

HOH

51C-109-

HOH

61C-110-

HOH

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Components

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


Mass: 1794.271 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: I
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / 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: 2.41 Å3/Da / Density % sol: 48.89 %
Crystal growTemperature: 296.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES sodium buffer (pH 7.5), 0.2 M sodium citrate, 22% isopropanol
PH range: 7.0-8.5

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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: Jun 18, 2016
RadiationMonochromator: Cu / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.026→19.56 Å / Num. obs: 3808 / % possible obs: 99.9 % / Redundancy: 36.8 % / Rmerge(I) obs: 0.03415 / Net I/σ(I): 24.3
Reflection shellResolution: 2.026→2.098 Å / Redundancy: 17.2 % / Rmerge(I) obs: 0.2676 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 365 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.026→19.557 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.48
RfactorNum. reflection% reflection
Rfree0.2466 663 10.11 %
Rwork0.2088 --
obs0.2128 3806 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.026→19.557 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms375 0 8 32 415
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005381
X-RAY DIFFRACTIONf_angle_d1.156501
X-RAY DIFFRACTIONf_dihedral_angle_d28.321243
X-RAY DIFFRACTIONf_chiral_restr0.06963
X-RAY DIFFRACTIONf_plane_restr0.00457
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0261-2.18240.38211250.27261188X-RAY DIFFRACTION99
2.1824-2.40160.27571310.23551167X-RAY DIFFRACTION100
2.4016-2.74830.23611370.2251173X-RAY DIFFRACTION100
2.7483-3.45950.26081320.19911177X-RAY DIFFRACTION100
3.4595-19.55750.20771380.1851189X-RAY DIFFRACTION100
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)
16.79142.25160.97963.05520.07811.8335-0.1769-0.3039-0.0796-0.2106-0.00730.1572-0.05040.21680.10790.21250.0212-0.01590.19620.00080.204321.524513.76726.583
24.0159-1.0297-1.46394.11982.79018.30320.0116-0.0866-0.00180.1620.1127-0.3074-0.1336-0.2417-0.15380.22060.0374-0.00030.21830.02510.277328.800921.1598-0.5735
33.98681.5179-1.258.904-2.38962.82510.03850.38850.2336-0.12990.0449-0.0815-0.0687-0.1731-0.05070.16560.029-0.01480.2396-0.02090.217220.500213.1359-5.8163
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 )

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