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- PDB-6dr4: X-ray crystallographic structure of a covalent trimer derived fro... -

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Basic information

Entry
Database: PDB / ID: 6dr4
TitleX-ray crystallographic structure of a covalent trimer derived from A-beta 17_36 containing the I31V point mutation
ComponentsORN-CYS-VAL-PHE-MEA-CYS-GLU-ASP-ORN-ALA-VAL-ILE-GLY-LEU-ORN-VAL
KeywordsDE NOVO PROTEIN / Amyloid / Alzheimers Disease / Abeta / oligomer
Function / homologyHEXANE-1,6-DIOL
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SAD / Resolution: 2.105 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 1.1Jan 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: ORN-CYS-VAL-PHE-MEA-CYS-GLU-ASP-ORN-ALA-VAL-ILE-GLY-LEU-ORN-VAL
C: ORN-CYS-VAL-PHE-MEA-CYS-GLU-ASP-ORN-ALA-VAL-ILE-GLY-LEU-ORN-VAL
B: ORN-CYS-VAL-PHE-MEA-CYS-GLU-ASP-ORN-ALA-VAL-ILE-GLY-LEU-ORN-VAL
D: ORN-CYS-VAL-PHE-MEA-CYS-GLU-ASP-ORN-ALA-VAL-ILE-GLY-LEU-ORN-VAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,4397
Polymers7,0854
Non-polymers3553
Water36020
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2320 Å2
ΔGint3 kcal/mol
Surface area5080 Å2
Unit cell
Length a, b, c (Å)57.685, 57.685, 94.683
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
ORN-CYS-VAL-PHE-MEA-CYS-GLU-ASP-ORN-ALA-VAL-ILE-GLY-LEU-ORN-VAL


Mass: 1771.152 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Chemical ChemComp-HEZ / HEXANE-1,6-DIOL


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 3.21 Å3/Da / Density % sol: 61.68 %
Crystal growTemperature: 296.15 K / Method: vapor diffusion, hanging drop
Details: 0.1 M tirs pH 9.0, 0.2 M magnesium chloride, 2.7 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: May 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.1→47.34 Å / Num. obs: 5880 / % possible obs: 99.9 % / Redundancy: 17.6 % / CC1/2: 1 / Net I/σ(I): 35.7
Reflection shellResolution: 2.1→2.17 Å / Redundancy: 13.9 % / Mean I/σ(I) obs: 2.7 / Num. unique obs: 461 / CC1/2: 0.886 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.105→27.591 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.83
RfactorNum. reflection% reflection
Rfree0.2638 1038 10.13 %
Rwork0.2259 --
obs0.2299 5880 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.105→27.591 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms488 0 24 20 532
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008520
X-RAY DIFFRACTIONf_angle_d1.201680
X-RAY DIFFRACTIONf_dihedral_angle_d26.373364
X-RAY DIFFRACTIONf_chiral_restr0.14180
X-RAY DIFFRACTIONf_plane_restr0.00480
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1048-2.21570.31081510.29221336X-RAY DIFFRACTION100
2.2157-2.35440.33781400.26841300X-RAY DIFFRACTION100
2.3544-2.53610.40841490.2871322X-RAY DIFFRACTION100
2.5361-2.79110.31721490.30411299X-RAY DIFFRACTION100
2.7911-3.19450.27081460.23261325X-RAY DIFFRACTION100
3.1945-4.02270.29591520.21331305X-RAY DIFFRACTION100
4.0227-27.59310.19671510.19251325X-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)
14.8294-3.97212.17445.861-0.06142.27290.1348-0.3408-0.72440.44020.13860.03740.3847-0.0573-0.23620.6326-0.0788-0.05810.36380.04530.51963.930819.674540.7929
26.91464.86210.89189.80532.16193.22060.08680.2337-0.8454-0.4009-0.6527-0.05390.43230.12390.34850.44610.0351-0.07740.3841-0.0140.511113.636529.699340.3148
33.45490.1565-0.20649.2607-1.14669.0789-0.1461-0.79640.76570.53760.3204-0.07490.5569-0.2868-0.00910.36850.0015-0.09390.42940.01320.36226.00827.803952.0909
48.3777-1.0333-3.67037.70660.09857.9929-0.461-0.1626-0.7516-0.27710.12571.00121.0018-0.44330.40950.5528-0.0703-0.00470.39210.04990.5113-2.377225.407628.8479
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 )
4X-RAY DIFFRACTION4chain 'D' and (resid 1 through 16 )

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