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- PDB-6dr5: X-ray crystallographic structure of a covalent trimer derived fro... -

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Basic information

Entry
Database: PDB / ID: 6dr5
TitleX-ray crystallographic structure of a covalent trimer derived from A-beta 17_36 containing the I31Chg point mutation
ComponentsORT-CYS-VAL-PHE-MEA-CYS-GLU-ASP-ORT-ALA-CHG-ILE-GLY-LEU-ORA-VAL
KeywordsDE NOVO PROTEIN / Amyloid / Alzheimers Disease / Abeta / oligomer
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SAD / Resolution: 2.079 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
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _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: ORT-CYS-VAL-PHE-MEA-CYS-GLU-ASP-ORT-ALA-CHG-ILE-GLY-LEU-ORA-VAL
B: ORT-CYS-VAL-PHE-MEA-CYS-GLU-ASP-ORT-ALA-CHG-ILE-GLY-LEU-ORA-VAL
C: ORT-CYS-VAL-PHE-MEA-CYS-GLU-ASP-ORT-ALA-CHG-ILE-GLY-LEU-ORA-VAL
D: ORT-CYS-VAL-PHE-MEA-CYS-GLU-ASP-ORT-ALA-CHG-ILE-GLY-LEU-ORA-VAL
E: ORT-CYS-VAL-PHE-MEA-CYS-GLU-ASP-ORT-ALA-CHG-ILE-GLY-LEU-ORA-VAL
F: ORT-CYS-VAL-PHE-MEA-CYS-GLU-ASP-ORT-ALA-CHG-ILE-GLY-LEU-ORA-VAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2229
Polymers10,8676
Non-polymers3553
Water68538
1
A: ORT-CYS-VAL-PHE-MEA-CYS-GLU-ASP-ORT-ALA-CHG-ILE-GLY-LEU-ORA-VAL
B: ORT-CYS-VAL-PHE-MEA-CYS-GLU-ASP-ORT-ALA-CHG-ILE-GLY-LEU-ORA-VAL
C: ORT-CYS-VAL-PHE-MEA-CYS-GLU-ASP-ORT-ALA-CHG-ILE-GLY-LEU-ORA-VAL
D: ORT-CYS-VAL-PHE-MEA-CYS-GLU-ASP-ORT-ALA-CHG-ILE-GLY-LEU-ORA-VAL
E: ORT-CYS-VAL-PHE-MEA-CYS-GLU-ASP-ORT-ALA-CHG-ILE-GLY-LEU-ORA-VAL
F: ORT-CYS-VAL-PHE-MEA-CYS-GLU-ASP-ORT-ALA-CHG-ILE-GLY-LEU-ORA-VAL
hetero molecules

A: ORT-CYS-VAL-PHE-MEA-CYS-GLU-ASP-ORT-ALA-CHG-ILE-GLY-LEU-ORA-VAL
B: ORT-CYS-VAL-PHE-MEA-CYS-GLU-ASP-ORT-ALA-CHG-ILE-GLY-LEU-ORA-VAL
C: ORT-CYS-VAL-PHE-MEA-CYS-GLU-ASP-ORT-ALA-CHG-ILE-GLY-LEU-ORA-VAL
D: ORT-CYS-VAL-PHE-MEA-CYS-GLU-ASP-ORT-ALA-CHG-ILE-GLY-LEU-ORA-VAL
E: ORT-CYS-VAL-PHE-MEA-CYS-GLU-ASP-ORT-ALA-CHG-ILE-GLY-LEU-ORA-VAL
F: ORT-CYS-VAL-PHE-MEA-CYS-GLU-ASP-ORT-ALA-CHG-ILE-GLY-LEU-ORA-VAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,44418
Polymers21,73512
Non-polymers7096
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z+1/31
Unit cell
Length a, b, c (Å)57.831, 57.831, 61.846
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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


Mass: 1811.216 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


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


Mass: 18.015 Da / Num. of mol.: 38 / 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: 2.75 Å3/Da / Density % sol: 55.23 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop
Details: 0.2 M ammonium acetate, 0.1 M bis-tris pH 5, 47% (v/v) 2-methyl-2,4-pentanediol

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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: Nov 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.079→38.9 Å / Num. obs: 13934 / % possible obs: 99.9 % / Redundancy: 24.8 % / CC1/2: 0.993 / Net I/σ(I): 78.3
Reflection shellResolution: 2.08→2.14 Å / Redundancy: 17.3 % / Mean I/σ(I) obs: 27.9 / Num. unique obs: 577 / CC1/2: 0.998 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.079→28.916 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2147 745 9.81 %
Rwork0.1718 --
obs0.176 13934 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.079→28.916 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms750 0 24 38 812
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008798
X-RAY DIFFRACTIONf_angle_d1.5661060
X-RAY DIFFRACTIONf_dihedral_angle_d30.282543
X-RAY DIFFRACTIONf_chiral_restr0.23125
X-RAY DIFFRACTIONf_plane_restr0.005121
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0792-2.15350.29111410.19811260X-RAY DIFFRACTION99
2.1535-2.23970.24681360.18651265X-RAY DIFFRACTION100
2.2397-2.34160.2271400.16291254X-RAY DIFFRACTION100
2.3416-2.4650.25241380.16571243X-RAY DIFFRACTION100
2.465-2.61930.22641370.1691269X-RAY DIFFRACTION100
2.6193-2.82140.20221390.18381237X-RAY DIFFRACTION100
2.8214-3.10510.22971350.16951263X-RAY DIFFRACTION100
3.1051-3.55370.21321380.16471255X-RAY DIFFRACTION100
3.5537-4.47460.16761470.14991251X-RAY DIFFRACTION100
4.4746-28.91830.22171160.18911270X-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)
14.5701-4.5213-2.61368.41534.15536.9656-0.0355-0.1203-0.21130.53940.2979-0.72420.48480.6299-0.08310.2360.0107-0.06410.2152-0.03980.318340.22462.24830.5631
23.94312.7728-4.11155.6826-2.93954.93690.1851-0.17410.3090.06840.05610.06080.11660.2542-0.28480.2039-0.0319-0.0270.2304-0.00730.191429.938211.596427.7735
35.3147-3.16753.95298.5153-1.14534.57330.24280.4267-0.1694-0.4826-0.0537-0.3307-0.49270.5336-0.09980.2048-0.02850.04810.2782-0.01630.251540.94629.239818.3264
44.86713.5715.95934.05724.14527.46370.049-0.377-0.12530.0682-0.25140.2778-0.1844-0.40980.11490.2210.0194-0.00520.21440.01540.203520.09129.576218.6688
54.2952-2.24462.08444.5835-3.77243.3721-0.0797-0.29230.17061.18160.15850.3371-0.4192-0.38280.10110.3397-0.02520.01930.23330.02340.279820.55652.119930.3632
63.78032.9063-3.85843.4385-3.31276.32870.22670.43560.24-0.0891-0.22990.1856-0.84020.2264-0.02790.3713-0.0698-0.04750.24990.02860.216335.878122.827729.8447
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 )
5X-RAY DIFFRACTION5chain 'E' and (resid 1 through 16 )
6X-RAY DIFFRACTION6chain 'F' and (resid 1 through 16 )

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