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- PDB-3q9j: AIIFL segment derived from Alzheimer's Amyloid-Beta displayed on ... -

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Basic information

Entry
Database: PDB / ID: 3q9j
TitleAIIFL segment derived from Alzheimer's Amyloid-Beta displayed on 42-membered macrocycle scaffold
ComponentsCyclic pseudo-peptide AIIFL(ORN)(HAO)YK(ORN)
KeywordsPROTEIN FIBRIL / beta sheet tetramer / macrocyclic peptide / beta-sheet mimic / amyloid-like oligomer
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.55 Å
AuthorsLiu, C. / Sawaya, M.R. / Eisenberg, D. / Nowick, J.S. / Cheng, P. / Zheng, J.
CitationJournal: J.Am.Chem.Soc. / Year: 2011
Title: Characteristics of Amyloid-Related Oligomers Revealed by Crystal Structures of Macrocyclic beta-Sheet Mimics.
Authors: Liu, C. / Sawaya, M.R. / Cheng, P.N. / Zheng, J. / Nowick, J.S. / Eisenberg, D.
History
DepositionJan 7, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0Nov 15, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_validate_main_chain_plane / pdbx_validate_polymer_linkage / pdbx_validate_rmsd_angle / struct_conn / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cyclic pseudo-peptide AIIFL(ORN)(HAO)YK(ORN)
B: Cyclic pseudo-peptide AIIFL(ORN)(HAO)YK(ORN)
C: Cyclic pseudo-peptide AIIFL(ORN)(HAO)YK(ORN)
D: Cyclic pseudo-peptide AIIFL(ORN)(HAO)YK(ORN)
E: Cyclic pseudo-peptide AIIFL(ORN)(HAO)YK(ORN)
F: Cyclic pseudo-peptide AIIFL(ORN)(HAO)YK(ORN)
G: Cyclic pseudo-peptide AIIFL(ORN)(HAO)YK(ORN)
H: Cyclic pseudo-peptide AIIFL(ORN)(HAO)YK(ORN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,59423
Polymers10,6538
Non-polymers94115
Water32418
1
A: Cyclic pseudo-peptide AIIFL(ORN)(HAO)YK(ORN)
B: Cyclic pseudo-peptide AIIFL(ORN)(HAO)YK(ORN)
C: Cyclic pseudo-peptide AIIFL(ORN)(HAO)YK(ORN)
D: Cyclic pseudo-peptide AIIFL(ORN)(HAO)YK(ORN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,75111
Polymers5,3264
Non-polymers4257
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3040 Å2
ΔGint-121 kcal/mol
Surface area3390 Å2
MethodPISA
2
E: Cyclic pseudo-peptide AIIFL(ORN)(HAO)YK(ORN)
F: Cyclic pseudo-peptide AIIFL(ORN)(HAO)YK(ORN)
G: Cyclic pseudo-peptide AIIFL(ORN)(HAO)YK(ORN)
H: Cyclic pseudo-peptide AIIFL(ORN)(HAO)YK(ORN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,84312
Polymers5,3264
Non-polymers5178
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2940 Å2
ΔGint-120 kcal/mol
Surface area3270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.780, 41.780, 63.060
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31

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Components

#1: Protein/peptide
Cyclic pseudo-peptide AIIFL(ORN)(HAO)YK(ORN)


Mass: 1331.581 Da / Num. of mol.: 8 / Mutation: G4F / Source method: obtained synthetically
Details: AIIFL segment derived from Alzheimer's Amyloid-Beta displayed on 42-membered macrocycle scaffold
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 2.98 Å3/Da / Density % sol: 58.76 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.00015 M zinc acetate, 0.1M MES pH 6.2, 12.5% PEG 8000, vapor diffusion, sitting drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9197, 0.9129
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 25, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.91971
20.91291
ReflectionResolution: 2.55→20 Å / Num. obs: 3979 / % possible obs: 98.1 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 71.594 Å2 / Rmerge(I) obs: 0.039 / Net I/σ(I): 14.57
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.55-2.620.5091.61423616100
2.62-2.690.6571.6119554799.5
2.69-2.770.622135959499
2.77-2.850.2992.81130502100
2.85-2.940.16951190528100
2.94-3.050.1316.61178522100
3.05-3.160.0978.61209536100
3.16-3.290.0968.21023450100
3.29-3.440.08610.2103646698.7
3.44-3.610.0419.988440499
3.61-3.80.03422.5101644599.8
3.8-4.030.02824.477636799.2
4.03-4.310.02331.878934999.1
4.31-4.660.02433.479535698.3
4.66-5.10.0223163129393.9
5.1-5.70.02228.956025694.8
5.7-6.580.0233.455824794.3
6.58-8.060.01940.748521695.6
8.06-11.410.01740.927812885.3
11.410.01843.31205659.6

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
BUSTER-TNTrefinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
XDSdata reduction
SHELXEmodel building
BUSTER2.8.0refinement
RefinementMethod to determine structure: MAD / Resolution: 2.55→18.18 Å / Cor.coef. Fo:Fc: 0.9314 / Cor.coef. Fo:Fc free: 0.928 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2226 398 10 %RANDOM
Rwork0.1756 ---
obs0.1805 3980 --
Displacement parametersBiso max: 289.96 Å2 / Biso mean: 73.1327 Å2 / Biso min: 30.59 Å2
Baniso -1Baniso -2Baniso -3
1--9.4762 Å20 Å20 Å2
2---9.4762 Å20 Å2
3---18.9523 Å2
Refine analyzeLuzzati coordinate error obs: 0.437 Å
Refinement stepCycle: LAST / Resolution: 2.55→18.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms752 0 30 18 800
Refine LS restraints
Refine-IDTypeNumberWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1902
X-RAY DIFFRACTIONt_trig_c_planes402
X-RAY DIFFRACTIONt_gen_planes2005
X-RAY DIFFRACTIONt_it62320
X-RAY DIFFRACTIONt_nbd15
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion805
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact9474
X-RAY DIFFRACTIONt_bond_d87120.01
X-RAY DIFFRACTIONt_angle_deg117521.12
X-RAY DIFFRACTIONt_omega_torsion4.15
X-RAY DIFFRACTIONt_other_torsion20.73
LS refinement shellResolution: 2.55→2.85 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.2844 113 9.96 %
Rwork0.1889 1021 -
all0.198 1134 -
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)
18.96493.78641.72214.5927-2.91261.60610.3426-0.7893-0.11440.47040.1666-0.0673-0.49430.6822-0.50920.1084-0.34210.1073-0.1724-0.0309-0.05063.41554.311815.103
22.36734.82973.976710.21-0.87274.04230.31490.4254-0.0762-1.07680.44860.094-0.64580.019-0.76350.189-0.21460.1123-0.1416-0.090.02511.875.1294.8661
3-1.33371.017-1.24021.68012.89131.0996-0.42080.705-0.88490.32810.4713-0.3056-0.51210.657-0.05040.1612-0.36430.1495-0.1201-0.05450.09312.317611.250910.7848
41.224-0.6395-1.94527.4271-2.68130-0.39870.41650.08860.38770.34490.6199-0.50660.06250.05380.1654-0.37210.0436-0.1068-0.09730.05693.585116.25629.1408
54.1205-1.60280.32836.62184.72940.0113-0.16350.31460.81110.450.22570.48450.5376-0.7096-0.06210.0852-0.4459-0.1332-0.10190.06980.0553-12.2325-11.315210.8198
60.45950.70523.257311.35011.70330.1922-0.51470.3408-0.16730.45260.527-0.66990.74340.0979-0.01230.1803-0.34380.008-0.12470.13530.0459-3.6263-16.30939.0453
77.00624.00250.37366.7807-0.29776.93230.3509-0.6264-0.02740.44880.009-0.23180.7434-0.4911-0.35980.1686-0.3191-0.1295-0.07980.0746-0.0104-3.3033-4.304515.0298
85.5765.48780.100412.34620.08793.77780.18410.69230.0588-0.92930.43250.21820.5721-0.333-0.61660.2206-0.2159-0.1105-0.13810.0612-0.0224-2.0254-5.11084.8009
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A1 - 10
2X-RAY DIFFRACTION2{ B|* }B1 - 10
3X-RAY DIFFRACTION3{ C|* }C1 - 10
4X-RAY DIFFRACTION4{ D|* }D1 - 10
5X-RAY DIFFRACTION5{ E|* }E1 - 10
6X-RAY DIFFRACTION6{ F|* }F1 - 10
7X-RAY DIFFRACTION7{ G|* }G1 - 10
8X-RAY DIFFRACTION8{ H|* }H1 - 10

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