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- PDB-3q9i: LVFFA segment from Alzheimer's Amyloid-Beta displayed on 42-membe... -

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Basic information

Entry
Database: PDB / ID: 3q9i
TitleLVFFA segment from Alzheimer's Amyloid-Beta displayed on 42-membered macrocycle scaffold, bromide derivative
ComponentsCyclic pseudo-peptide LV(4BF)FA(ORN)(HAO)LK(ORN)
KeywordsPROTEIN FIBRIL / beta sheet tetramer / beta strand
Function / homologyISOPROPYL ALCOHOL
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.99 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_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 / _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 LV(4BF)FA(ORN)(HAO)LK(ORN)
B: Cyclic pseudo-peptide LV(4BF)FA(ORN)(HAO)LK(ORN)
C: Cyclic pseudo-peptide LV(4BF)FA(ORN)(HAO)LK(ORN)
D: Cyclic pseudo-peptide LV(4BF)FA(ORN)(HAO)LK(ORN)
E: Cyclic pseudo-peptide LV(4BF)FA(ORN)(HAO)LK(ORN)
F: Cyclic pseudo-peptide LV(4BF)FA(ORN)(HAO)LK(ORN)
G: Cyclic pseudo-peptide LV(4BF)FA(ORN)(HAO)LK(ORN)
H: Cyclic pseudo-peptide LV(4BF)FA(ORN)(HAO)LK(ORN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,68820
Polymers11,0448
Non-polymers64512
Water77543
1
A: Cyclic pseudo-peptide LV(4BF)FA(ORN)(HAO)LK(ORN)
B: Cyclic pseudo-peptide LV(4BF)FA(ORN)(HAO)LK(ORN)
C: Cyclic pseudo-peptide LV(4BF)FA(ORN)(HAO)LK(ORN)
D: Cyclic pseudo-peptide LV(4BF)FA(ORN)(HAO)LK(ORN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,94011
Polymers5,5224
Non-polymers4187
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Cyclic pseudo-peptide LV(4BF)FA(ORN)(HAO)LK(ORN)
B: Cyclic pseudo-peptide LV(4BF)FA(ORN)(HAO)LK(ORN)
E: Cyclic pseudo-peptide LV(4BF)FA(ORN)(HAO)LK(ORN)
F: Cyclic pseudo-peptide LV(4BF)FA(ORN)(HAO)LK(ORN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,81610
Polymers5,5224
Non-polymers2946
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Cyclic pseudo-peptide LV(4BF)FA(ORN)(HAO)LK(ORN)
D: Cyclic pseudo-peptide LV(4BF)FA(ORN)(HAO)LK(ORN)
G: Cyclic pseudo-peptide LV(4BF)FA(ORN)(HAO)LK(ORN)
H: Cyclic pseudo-peptide LV(4BF)FA(ORN)(HAO)LK(ORN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,87210
Polymers5,5224
Non-polymers3516
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.980, 58.980, 128.511
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein/peptide
Cyclic pseudo-peptide LV(4BF)FA(ORN)(HAO)LK(ORN)


Mass: 1380.450 Da / Num. of mol.: 8 / Source method: obtained synthetically
Details: LVFFA segment from Alzheimer's Amyloid-Beta displayed on 42-membered macrocycle scaffold
#2: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / Isopropyl alcohol


Mass: 60.095 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 43 / 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: 5.06 Å3/Da / Density % sol: 75.69 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.1 M sodium acetate pH 4.6, 0.17 mM calcium chloride dehydrate, 20% (v/v) 2-propanol, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 25, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2→80 Å / Num. obs: 16219 / % possible obs: 100 % / Redundancy: 13.6 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 14.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2-2.07140.4781100
2.07-2.15140.3451100
2.15-2.2513.90.2831100
2.25-2.3713.90.2321100
2.37-2.5213.80.1621100
2.52-2.7113.80.1221100
2.71-2.9913.70.11100
2.99-3.4213.40.0681100
3.42-4.31130.044199.9
4.31-8012.40.037199.8

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
DENZOdata reduction
RefinementMethod to determine structure: SAD / Resolution: 1.99→53.6 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.948 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 4.47 / SU ML: 0.06 / Cross valid method: THROUGHOUT / ESU R: 0.105 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21827 808 5 %RANDOM
Rwork0.19581 ---
obs0.19682 15269 99.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.798 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å20 Å20 Å2
2--0.3 Å20 Å2
3----0.61 Å2
Refinement stepCycle: LAST / Resolution: 1.99→53.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms744 0 33 43 820
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.022789
X-RAY DIFFRACTIONr_bond_other_d0.0070.02598
X-RAY DIFFRACTIONr_angle_refined_deg1.162.515933
X-RAY DIFFRACTIONr_angle_other_deg0.62331378
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.74524
X-RAY DIFFRACTIONr_dihedral_angle_2_deg11.177208
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.0451580
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0830.296
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.02648
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02224
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7851.5296
X-RAY DIFFRACTIONr_mcbond_other0.6691.5176
X-RAY DIFFRACTIONr_mcangle_it2.4582376
X-RAY DIFFRACTIONr_scbond_it3.7443493
X-RAY DIFFRACTIONr_scangle_it4.754.5557
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.992→2.044 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 71 -
Rwork0.228 1033 -
obs--94.04 %
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)
11.30350.1829-0.55856.52610.30773.5755-0.1280.0227-0.1169-0.09320.0416-0.10050.1916-0.1520.08640.0268-0.00860.02990.06940.00910.04351.9676.13315.172
20.01710.0605-0.18714.90410.77052.898-0.0378-0.0725-0.03830.0783-0.16680.08760.30740.420.20450.04280.06890.04080.14840.07760.04943.6264.19724.21
31.2541-0.89510.16755.576-0.43794.182-0.0773-0.2388-0.1308-0.1307-0.05280.0359-0.00290.18240.13010.01110.020.01140.08910.02570.022311.5969.46717.731
43.6092-2.6691-1.46475.81930.25672.5035-0.04070.138-0.0354-0.13530.0452-0.0380.1818-0.2401-0.00450.025-0.01830.00890.0636-0.00590.01047.7179.8349.04
51.23260.11640.1912.2266-0.18422.0893-0.03060.08510.0838-0.01260.08240.0123-0.03030.0822-0.05170.00810.00020.00360.08910.00850.021-5.35713.41420.919
61.38421.27951.26593.23521.15845.637-0.0642-0.1733-0.04480.053-0.16410.0046-0.0168-0.01950.22830.02040.01240.00990.09950.02040.0187-2.0958.39328.79
72.7865-1.97291.57962.0849-1.83382.8877-0.11740.15270.0405-0.0203-0.0125-0.02280.0447-0.02540.12990.02890.00050.00180.07470.01180.012311.89715.6544.927
83.0881-1.03080.99842.12710.56051.8082-0.0703-0.14550.1078-0.01570.03970.0028-0.10530.05170.03060.00630.0016-0.00080.06320.0040.00817.37518.38612.702
933.4944-0.582730.6492-0.19686.6751160.23920.0001-1.0931.11960.01790.0633-0.06050.7850.2509-0.06340.140.0133-0.01460.2125-0.02710.15237.70519.97712.671
101.51620.2663-0.56320.1823-0.23830.32950.00770.0689-0.01260.0523-0.01210.0002-0.04050.00790.00440.06730.0387-0.00770.0532-0.00920.002310.3316.29711.244
1172.321-70.5391-0.5421133.501141.237431.475-2.1524-1.30670.8685-0.9941.37232.256-0.36321.65710.78010.44420.123-0.20190.3713-0.11360.31623.74615.24224.23
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 9
2X-RAY DIFFRACTION2B1 - 9
3X-RAY DIFFRACTION3C1 - 9
4X-RAY DIFFRACTION4D1 - 9
5X-RAY DIFFRACTION5E1 - 9
6X-RAY DIFFRACTION6F1 - 9
7X-RAY DIFFRACTION7G1 - 9
8X-RAY DIFFRACTION8H1 - 9
9X-RAY DIFFRACTION9D11
10X-RAY DIFFRACTION10G11 - 26
11X-RAY DIFFRACTION11B11

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