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- PDB-6dr6: X-ray crystallographic structure of a covalent trimer derived fro... -

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Basic information

Entry
Database: PDB / ID: 6dr6
TitleX-ray crystallographic structure of a covalent trimer derived from A-beta 17_36 containing the F20Cha point mutation
ComponentsORT-CYS-VAL-PHE-XXX-CYS-GLU-ASP-ORT-ALA-ILE-ILE-GLY-LEU-ORA-VAL
KeywordsDE NOVO PROTEIN / Amyloid / Alzheimers Disease / Abeta / oligomer
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SAD / Resolution: 2.608 Å
AuthorsSalveson, P.J. / Nowick, J.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)097562 United States
CitationJournal: J. Am. Chem. Soc. / Year: 2018
Title: Repurposing Triphenylmethane Dyes to Bind to Trimers Derived from A beta.
Authors: Salveson, P.J. / Haerianardakani, S. / Thuy-Boun, A. / Yoo, S. / Kreutzer, A.G. / Demeler, B. / Nowick, J.S.
History
DepositionJun 11, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2018Provider: repository / Type: Initial release
Revision 2.0Jan 1, 2020Group: Author supporting evidence / Data collection / Polymer sequence
Category: chem_comp / entity_poly / pdbx_audit_support
Item: _chem_comp.type / _entity_poly.pdbx_seq_one_letter_code_can / _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: ORT-CYS-VAL-PHE-XXX-CYS-GLU-ASP-ORT-ALA-ILE-ILE-GLY-LEU-ORA-VAL
D: ORT-CYS-VAL-PHE-XXX-CYS-GLU-ASP-ORT-ALA-ILE-ILE-GLY-LEU-ORA-VAL
B: ORT-CYS-VAL-PHE-XXX-CYS-GLU-ASP-ORT-ALA-ILE-ILE-GLY-LEU-ORA-VAL
C: ORT-CYS-VAL-PHE-XXX-CYS-GLU-ASP-ORT-ALA-ILE-ILE-GLY-LEU-ORA-VAL


Theoretical massNumber of molelcules
Total (without water)7,1654
Polymers7,1654
Non-polymers00
Water1267
1
A: ORT-CYS-VAL-PHE-XXX-CYS-GLU-ASP-ORT-ALA-ILE-ILE-GLY-LEU-ORA-VAL
B: ORT-CYS-VAL-PHE-XXX-CYS-GLU-ASP-ORT-ALA-ILE-ILE-GLY-LEU-ORA-VAL
C: ORT-CYS-VAL-PHE-XXX-CYS-GLU-ASP-ORT-ALA-ILE-ILE-GLY-LEU-ORA-VAL

A: ORT-CYS-VAL-PHE-XXX-CYS-GLU-ASP-ORT-ALA-ILE-ILE-GLY-LEU-ORA-VAL
B: ORT-CYS-VAL-PHE-XXX-CYS-GLU-ASP-ORT-ALA-ILE-ILE-GLY-LEU-ORA-VAL
C: ORT-CYS-VAL-PHE-XXX-CYS-GLU-ASP-ORT-ALA-ILE-ILE-GLY-LEU-ORA-VAL


Theoretical massNumber of molelcules
Total (without water)10,7476
Polymers10,7476
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area3600 Å2
ΔGint-37 kcal/mol
Surface area6310 Å2
MethodPISA
2
D: ORT-CYS-VAL-PHE-XXX-CYS-GLU-ASP-ORT-ALA-ILE-ILE-GLY-LEU-ORA-VAL
x 6


Theoretical massNumber of molelcules
Total (without water)10,7476
Polymers10,7476
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/21
crystal symmetry operation11_555-x+y,y,-z+1/21
crystal symmetry operation12_565x,x-y+1,-z+1/21
Buried area3750 Å2
ΔGint-43 kcal/mol
Surface area6020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.058, 58.058, 95.609
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein/peptide
ORT-CYS-VAL-PHE-XXX-CYS-GLU-ASP-ORT-ALA-ILE-ILE-GLY-LEU-ORA-VAL


Mass: 1791.226 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 3.25 Å3/Da / Density % sol: 62.11 %
Crystal growTemperature: 296.15 K / Method: vapor diffusion, hanging drop
Details: 0.1 M tris pH 7.5, ).2 M magnesium chloride, 3.9 M 1,6-hexanediol

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Data collection

DiffractionMean temperature: 123 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 92 / Detector: CCD / Date: Feb 9, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.608→34.645 Å / Num. obs: 5520 / % possible obs: 100 % / Redundancy: 75.4 % / CC1/2: 1 / Net I/σ(I): 57.4
Reflection shellResolution: 2.62→2.72 Å / Num. unique all: 1234 / CC1/2: 0.993

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.608→34.645 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.2
RfactorNum. reflection% reflection
Rfree0.2768 561 10.16 %
Rwork0.2421 --
obs0.2459 5520 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.608→34.645 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms492 0 0 7 499
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004503
X-RAY DIFFRACTIONf_angle_d1.283666
X-RAY DIFFRACTIONf_dihedral_angle_d31.985369
X-RAY DIFFRACTIONf_chiral_restr0.20684
X-RAY DIFFRACTIONf_plane_restr0.00276
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6079-2.87020.38121420.31891234X-RAY DIFFRACTION100
2.8702-3.28530.31541410.2891241X-RAY DIFFRACTION100
3.2853-4.1380.30271380.25661237X-RAY DIFFRACTION100
4.138-34.64790.2311400.20291247X-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)
15.4587-0.53761.07995.5174-1.08992.0652-0.30240.597-0.67660.3505-0.19260.23390.32890.75880.52390.54360.0260.10.6089-0.05120.70143.677820.111741.3767
22.50610.8291-0.00334.65670.11371.3967-0.0359-1.0527-0.29480.1062-0.2024-0.2985-0.257-0.15790.22660.3430.0584-0.0780.68320.08650.416.107328.375652.6788
35.97131.1456-0.11439.626-0.9324.38910.00360.6267-0.1396-0.06750.1153-0.5320.43010.2419-0.03350.50490.07850.04570.6961-0.04470.720413.709129.932340.9557
44.89992.3742-3.72343.2044-3.00923.5510.2781-0.1771-0.0435-0.9652-0.7601-0.53180.38440.49840.34240.8368-0.10880.10190.81-0.07580.4889-1.833225.472729.9952
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 16 )A1 - 16
2X-RAY DIFFRACTION2chain 'B' and (resid 1 through 16 )B1 - 16
3X-RAY DIFFRACTION3chain 'C' and (resid 1 through 16 )C1 - 16
4X-RAY DIFFRACTION4chain 'D' and (resid 1 through 16 )D1 - 16

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