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- PDB-3q9h: LVFFA segment from Alzheimer's Amyloid-Beta displayed on 42-membe... -

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Basic information

Entry
Database: PDB / ID: 3q9h
TitleLVFFA segment from Alzheimer's Amyloid-Beta displayed on 42-membered macrocycle scaffold
ComponentsCyclic pseudo-peptide LVFFA(ORN)(HAO)LK(ORN)
KeywordsPROTEIN FIBRIL / beta sheet tetramer / macrocyclic peptide / beta-sheet mimetic
Function / homology1,4-BUTANEDIOL
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.25 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_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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)12,44130
Polymers10,4128
Non-polymers2,02822
Water54030
1
A: Cyclic pseudo-peptide LVFFA(ORN)(HAO)LK(ORN)
B: Cyclic pseudo-peptide LVFFA(ORN)(HAO)LK(ORN)
C: Cyclic pseudo-peptide LVFFA(ORN)(HAO)LK(ORN)
D: Cyclic pseudo-peptide LVFFA(ORN)(HAO)LK(ORN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,85111
Polymers5,2064
Non-polymers6457
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Cyclic pseudo-peptide LVFFA(ORN)(HAO)LK(ORN)
B: Cyclic pseudo-peptide LVFFA(ORN)(HAO)LK(ORN)
E: Cyclic pseudo-peptide LVFFA(ORN)(HAO)LK(ORN)
F: Cyclic pseudo-peptide LVFFA(ORN)(HAO)LK(ORN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,03913
Polymers5,2064
Non-polymers8339
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Cyclic pseudo-peptide LVFFA(ORN)(HAO)LK(ORN)
D: Cyclic pseudo-peptide LVFFA(ORN)(HAO)LK(ORN)
G: Cyclic pseudo-peptide LVFFA(ORN)(HAO)LK(ORN)
H: Cyclic pseudo-peptide LVFFA(ORN)(HAO)LK(ORN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,40217
Polymers5,2064
Non-polymers1,19513
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.860, 57.860, 129.738
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein/peptide
Cyclic pseudo-peptide LVFFA(ORN)(HAO)LK(ORN)


Mass: 1301.554 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-BU1 / 1,4-BUTANEDIOL


Mass: 90.121 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C4H10O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 5.21 Å3/Da / Density % sol: 76.41 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.2M Lithium Sulfate, 0.1M MES pH 6.0, 20% 1,4-butanediol, 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: 0.9791 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: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.25→100 Å / Num. all: 11013 / Num. obs: 11013 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Biso Wilson estimate: 59.9 Å2 / Rmerge(I) obs: 0.073 / Χ2: 1.086 / Net I/σ(I): 12.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.25-2.333.40.4710821.129199.6
2.33-2.423.50.37410571.104199.3
2.42-2.533.50.25910931.07199.9
2.53-2.673.40.17310781.08199.8
2.67-2.833.40.14210841.089199.2
2.83-3.053.40.09911091.071199.8
3.05-3.363.40.0810871.061199.3
3.36-3.853.30.07111221.061199.6
3.85-4.853.10.05711321.177198.7
4.85-1003.10.05411691.024193.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
BUSTER-TNTrefinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
REFMACphasing
BUSTER2.8.0refinement
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.25→28.24 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.9258 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2216 524 4.77 %RANDOM
Rwork0.2053 ---
obs0.2061 10974 --
Displacement parametersBiso max: 113.19 Å2 / Biso mean: 55.4961 Å2 / Biso min: 19.61 Å2
Baniso -1Baniso -2Baniso -3
1--4.9316 Å20 Å20 Å2
2---4.9316 Å20 Å2
3---9.8633 Å2
Refine analyzeLuzzati coordinate error obs: 0.282 Å
Refinement stepCycle: LAST / Resolution: 2.25→28.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms736 0 126 30 892
Refine LS restraints
Refine-IDTypeNumberWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1542
X-RAY DIFFRACTIONt_trig_c_planes322
X-RAY DIFFRACTIONt_gen_planes1525
X-RAY DIFFRACTIONt_it67320
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion565
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_contact7774
X-RAY DIFFRACTIONt_bond_d86420.01
X-RAY DIFFRACTIONt_angle_deg112121.27
X-RAY DIFFRACTIONt_omega_torsion4.09
X-RAY DIFFRACTIONt_other_torsion16.27
LS refinement shellResolution: 2.25→2.46 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.225 122 4.78 %
Rwork0.197 2430 -
all0.1983 2552 -
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)
12.80021.42160.08350.0818-1.59831.2245-0.16460.3408-0.6631-0.11240.1929-0.10220.2669-0.319-0.0282-0.1883-0.02740.1064-0.0414-0.0209-0.03871.38455.86415.152
20-1.73111.69212.073-1.31253.4120.1075-0.0459-0.70280.1567-0.04520.20670.14780.3194-0.0623-0.1140.08570.12970.01170.14160.11582.93923.296924.1903
30.4453-2.54671.04391.5355-0.10821.512-0.2106-0.0936-0.53870.07580.00690.27590.0510.40740.2037-0.20470.00780.0848-0.00780.0099-0.063711.51739.330317.9787
41.0818-0.16544.23781.9525-0.8711.7441-0.1960.2034-0.5318-0.14840.349-0.160.0128-0.2415-0.153-0.111-0.08640.14710.042-0.071-0.00657.6619.01039.2575
50.186-1.1902-0.1141.24920.87132.163-0.13650.01870.1137-0.04550.0732-0.0834-0.00780.19390.0633-0.09440.00940.03330.0744-0.0061-0.0469-5.610912.620520.8457
60.2888-0.32851.29183.33861.04441.9037-0.0346-0.2023-0.26-0.039-0.2096-0.2820.0378-0.07570.2442-0.1095-0.03870.0610.01510.0402-0.108-2.39637.677528.7761
71.8534-1.70040.42582.0312-0.04852.2976-0.08140.25760.03970.121-0.0099-0.0452-0.1121-0.15040.0913-0.12760.02310.03050.00520.0218-0.133411.610114.78844.747
81.44723.26570.10731.4715-0.99244.5879-0.0855-0.19820.12410.29880.02780.0865-0.142-0.2240.0576-0.0840.01920.00470.06240.0321-0.042917.062117.610212.6777
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|1 - A|9 }A1 - 9
2X-RAY DIFFRACTION2{ B|1 - B|9 }B1 - 9
3X-RAY DIFFRACTION3{ C|1 - C|9 }C1 - 9
4X-RAY DIFFRACTION4{ D|1 - D|9 }D1 - 9
5X-RAY DIFFRACTION5{ E|1 - E|9 }E1 - 9
6X-RAY DIFFRACTION6{ F|1 - F|9 }F1 - 9
7X-RAY DIFFRACTION7{ G|1 - G|9 }G1 - 9
8X-RAY DIFFRACTION8{ H|1 - H|9 }H1 - 9

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