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- PDB-5w4h: X-ray crystallographic structure of a beta-hairpin peptide mimic ... -

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Basic information

Entry
Database: PDB / ID: 5w4h
TitleX-ray crystallographic structure of a beta-hairpin peptide mimic derived from Abeta 16-36. Synchrotron data set. (ORN)KLV(MEA)FAE(ORN)AIIGLMV.
ComponentsA-beta 17_36 peptide: 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.718 Å
AuthorsKreutzer, A.G. / 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: 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
Revision 1.3Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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: A-beta 17_36 peptide: ORN-LYS-LEU-VAL-MEA-PHE-ALA-GLU-ORN-ALA-ILE-ILE-GLY-LEU-MET-VAL
B: A-beta 17_36 peptide: ORN-LYS-LEU-VAL-MEA-PHE-ALA-GLU-ORN-ALA-ILE-ILE-GLY-LEU-MET-VAL
C: A-beta 17_36 peptide: ORN-LYS-LEU-VAL-MEA-PHE-ALA-GLU-ORN-ALA-ILE-ILE-GLY-LEU-MET-VAL


Theoretical massNumber of molelcules
Total (without water)5,3833
Polymers5,3833
Non-polymers00
Water59433
1
A: A-beta 17_36 peptide: ORN-LYS-LEU-VAL-MEA-PHE-ALA-GLU-ORN-ALA-ILE-ILE-GLY-LEU-MET-VAL
B: A-beta 17_36 peptide: ORN-LYS-LEU-VAL-MEA-PHE-ALA-GLU-ORN-ALA-ILE-ILE-GLY-LEU-MET-VAL
C: A-beta 17_36 peptide: ORN-LYS-LEU-VAL-MEA-PHE-ALA-GLU-ORN-ALA-ILE-ILE-GLY-LEU-MET-VAL

A: A-beta 17_36 peptide: ORN-LYS-LEU-VAL-MEA-PHE-ALA-GLU-ORN-ALA-ILE-ILE-GLY-LEU-MET-VAL
B: A-beta 17_36 peptide: ORN-LYS-LEU-VAL-MEA-PHE-ALA-GLU-ORN-ALA-ILE-ILE-GLY-LEU-MET-VAL
C: A-beta 17_36 peptide: ORN-LYS-LEU-VAL-MEA-PHE-ALA-GLU-ORN-ALA-ILE-ILE-GLY-LEU-MET-VAL


Theoretical massNumber of molelcules
Total (without water)10,7666
Polymers10,7666
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation13_556y,x,-z+11
Buried area5010 Å2
ΔGint-28 kcal/mol
Surface area5360 Å2
MethodPISA
2
A: A-beta 17_36 peptide: ORN-LYS-LEU-VAL-MEA-PHE-ALA-GLU-ORN-ALA-ILE-ILE-GLY-LEU-MET-VAL
B: A-beta 17_36 peptide: ORN-LYS-LEU-VAL-MEA-PHE-ALA-GLU-ORN-ALA-ILE-ILE-GLY-LEU-MET-VAL
C: A-beta 17_36 peptide: ORN-LYS-LEU-VAL-MEA-PHE-ALA-GLU-ORN-ALA-ILE-ILE-GLY-LEU-MET-VAL
x 24


Theoretical massNumber of molelcules
Total (without water)129,18872
Polymers129,18872
Non-polymers00
Water1,29772
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_656-x+1,y,-z+11
crystal symmetry operation4_566x,-y+1,-z+11
crystal symmetry operation5_555z,x,y1
crystal symmetry operation6_566z,-x+1,-y+11
crystal symmetry operation7_665-z+1,-x+1,y1
crystal symmetry operation8_656-z+1,x,-y+11
crystal symmetry operation9_555y,z,x1
crystal symmetry operation10_656-y+1,z,-x+11
crystal symmetry operation11_566y,-z+1,-x+11
crystal symmetry operation12_665-y+1,-z+1,x1
crystal symmetry operation13_556y,x,-z+11
crystal symmetry operation14_666-y+1,-x+1,-z+11
crystal symmetry operation15_565y,-x+1,z1
crystal symmetry operation16_655-y+1,x,z1
crystal symmetry operation17_556x,z,-y+11
crystal symmetry operation18_655-x+1,z,y1
crystal symmetry operation19_666-x+1,-z+1,-y+11
crystal symmetry operation20_565x,-z+1,y1
crystal symmetry operation21_556z,y,-x+11
crystal symmetry operation22_565z,-y+1,x1
crystal symmetry operation23_655-z+1,y,x1
crystal symmetry operation24_666-z+1,-y+1,-x+11
Buried area84180 Å2
ΔGint-539 kcal/mol
Surface area40200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.540, 67.540, 67.540
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-110-

HOH

21B-108-

HOH

31C-112-

HOH

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Components

#1: Protein/peptide A-beta 17_36 peptide: 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 2.38 Å3/Da / Density % sol: 48.42 %
Crystal growTemperature: 296.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES buffer (pH 7.0), 0.25 M magnesium chloride, 34% isopropanol
PH range: 7.0-8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.998 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 2, 2015
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.998 Å / Relative weight: 1
ReflectionResolution: 1.718→67.54 Å / Num. obs: 6026 / % possible obs: 99.34 % / Redundancy: 9.5 % / Rmerge(I) obs: 0.009274 / Net I/σ(I): 19.79
Reflection shellResolution: 1.718→1.78 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.2266 / Num. unique obs: 580 / % possible all: 97.97

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Processing

Software
NameVersionClassification
PHENIX1.11.1-2575refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5W4I

5w4i


Resolution: 1.718→67.54 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.15
RfactorNum. reflection% reflection
Rfree0.2371 603 10.01 %
Rwork0.2023 --
obs0.2058 6025 99.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.718→67.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms375 0 0 33 408
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015381
X-RAY DIFFRACTIONf_angle_d1.826501
X-RAY DIFFRACTIONf_dihedral_angle_d29.113243
X-RAY DIFFRACTIONf_chiral_restr0.08563
X-RAY DIFFRACTIONf_plane_restr0.01157
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7177-1.89060.33751440.26911297X-RAY DIFFRACTION99
1.8906-2.16420.25181480.20181327X-RAY DIFFRACTION100
2.1642-2.72670.23391500.2291349X-RAY DIFFRACTION100
2.7267-67.5920.22671610.18891449X-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)
13.44984.4487-2.75998.2453-1.71014.75690.1773-0.33350.49050.1612-0.06750.23190.0009-0.17740.02720.25720.04380.02740.25110.02530.234712.362520.082840.3202
24.0673-2.7550.97214.1146-0.44045.2124-0.3076-0.1255-0.50050.26980.43520.50590.8075-0.09-0.0180.2952-0.0051-0.03410.40850.06020.42685.162212.860333.2819
35.63142.1672.084.65974.02694.56850.28860.19190.0831-0.3588-0.26490.0018-0.7332-0.2711-0.14320.36380.06150.03350.29990.02510.265113.320920.882927.887
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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