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- PDB-5suu: X-ray crystallographic structure of a covalent trimer derived fro... -

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Basic information

Entry
Database: PDB / ID: 5suu
TitleX-ray crystallographic structure of a covalent trimer derived from A-beta 17-36. X-ray diffractometer data set. (ORN)CVFFCED(ORN)AII(SAR)L(ORN)V.
Components16mer A-beta peptide: ORN-CYS-VAL-PHE-PHE-CYS-GLU-ASP-ORN-ALA-ILE-ILE-SAR-LEU-ORN-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: 2.032 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: J.Am.Chem.Soc. / Year: 2017
Title: Stabilization, Assembly, and Toxicity of Trimers Derived from A beta.
Authors: Kreutzer, A.G. / Yoo, S. / Spencer, R.K. / Nowick, J.S.
History
DepositionAug 3, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Advisory / Author supporting evidence
Category: pdbx_audit_support / pdbx_validate_polymer_linkage
Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 27, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author / database_2 / struct_conn
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _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 / _citation_author.identifier_ORCID / _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: 16mer A-beta peptide: ORN-CYS-VAL-PHE-PHE-CYS-GLU-ASP-ORN-ALA-ILE-ILE-SAR-LEU-ORN-VAL
B: 16mer A-beta peptide: ORN-CYS-VAL-PHE-PHE-CYS-GLU-ASP-ORN-ALA-ILE-ILE-SAR-LEU-ORN-VAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,8397
Polymers3,5702
Non-polymers2695
Water18010
1
A: 16mer A-beta peptide: ORN-CYS-VAL-PHE-PHE-CYS-GLU-ASP-ORN-ALA-ILE-ILE-SAR-LEU-ORN-VAL
hetero molecules

A: 16mer A-beta peptide: ORN-CYS-VAL-PHE-PHE-CYS-GLU-ASP-ORN-ALA-ILE-ILE-SAR-LEU-ORN-VAL
hetero molecules

A: 16mer A-beta peptide: ORN-CYS-VAL-PHE-PHE-CYS-GLU-ASP-ORN-ALA-ILE-ILE-SAR-LEU-ORN-VAL
hetero molecules

B: 16mer A-beta peptide: ORN-CYS-VAL-PHE-PHE-CYS-GLU-ASP-ORN-ALA-ILE-ILE-SAR-LEU-ORN-VAL
hetero molecules

B: 16mer A-beta peptide: ORN-CYS-VAL-PHE-PHE-CYS-GLU-ASP-ORN-ALA-ILE-ILE-SAR-LEU-ORN-VAL
hetero molecules

B: 16mer A-beta peptide: ORN-CYS-VAL-PHE-PHE-CYS-GLU-ASP-ORN-ALA-ILE-ILE-SAR-LEU-ORN-VAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,51721
Polymers10,7116
Non-polymers80615
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation7_445x-1/3,y-2/3,z+1/31
crystal symmetry operation8_555-y+2/3,x-y+1/3,z+1/31
crystal symmetry operation9_455-x+y-1/3,-x+1/3,z+1/31
Buried area4770 Å2
ΔGint-110 kcal/mol
Surface area6660 Å2
MethodPISA
2
A: 16mer A-beta peptide: ORN-CYS-VAL-PHE-PHE-CYS-GLU-ASP-ORN-ALA-ILE-ILE-SAR-LEU-ORN-VAL
hetero molecules
x 6
B: 16mer A-beta peptide: ORN-CYS-VAL-PHE-PHE-CYS-GLU-ASP-ORN-ALA-ILE-ILE-SAR-LEU-ORN-VAL
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)23,03442
Polymers21,42212
Non-polymers1,61230
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_556y,x,-z+11
crystal symmetry operation5_556x-y,-y,-z+11
crystal symmetry operation6_556-x,-x+y,-z+11
crystal symmetry operation7_445x-1/3,y-2/3,z+1/31
crystal symmetry operation8_555-y+2/3,x-y+1/3,z+1/31
crystal symmetry operation9_455-x+y-1/3,-x+1/3,z+1/31
crystal symmetry operation16_445y-2/3,x-1/3,-z+2/31
crystal symmetry operation17_555x-y+1/3,-y+2/3,-z+2/31
crystal symmetry operation18_545-x+1/3,-x+y-1/3,-z+2/31
Buried area11190 Å2
ΔGint-258 kcal/mol
Surface area12050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.236, 50.236, 64.802
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11B-102-

CL

21A-201-

HOH

31B-201-

HOH

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Components

#1: Protein/peptide 16mer A-beta peptide: ORN-CYS-VAL-PHE-PHE-CYS-GLU-ASP-ORN-ALA-ILE-ILE-SAR-LEU-ORN-VAL


Mass: 1785.178 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: 16mer peptide derived from A-beta 17-36 / Source: (synth.) Homo sapiens (human)
#2: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: I
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 2.2 Å3/Da / Density % sol: 44.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0.1 M HEPES buffer at pH 6.5, 32% Jeffamine M-600

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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 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.032→25.12 Å / Num. obs: 2159 / % possible obs: 98.01 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.05975 / Net I/σ(I): 33.18
Reflection shellResolution: 2.032→2.096 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.1306 / Mean I/σ(I) obs: 12.05 / % possible all: 90.87

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.032→25.118 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 27.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2398 344 8.94 %
Rwork0.2163 --
obs0.2184 3847 97.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.032→25.118 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms246 0 5 10 261
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007252
X-RAY DIFFRACTIONf_angle_d1.236332
X-RAY DIFFRACTIONf_dihedral_angle_d31.721124
X-RAY DIFFRACTIONf_chiral_restr0.04140
X-RAY DIFFRACTIONf_plane_restr0.00842
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.032-2.55970.26751710.21771716X-RAY DIFFRACTION95
2.5597-25.11990.22741730.21571787X-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)
15.82650.24143.98326.4682-0.37578.7407-0.7721-0.36980.74140.43480.24990.1762-0.3336-0.26190.47940.23030.0432-0.01180.2075-0.05370.1429-2.45515.9066.9049
24.8230.6912-0.99262.1167-0.19691.99160.04390.0613-0.308-0.2062-0.039-0.1650.07750.03990.21980.0727-0.01210.03130.1026-0.13650.0918-0.3422.58673.5208
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 15 )
2X-RAY DIFFRACTION2chain 'B' and (resid 1 through 15 )

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