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- PDB-3q9g: VQIVY segment from Alzheimer's tau displayed on 42-membered macro... -

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Basic information

Entry
Database: PDB / ID: 3q9g
TitleVQIVY segment from Alzheimer's tau displayed on 42-membered macrocycle scaffold
ComponentsCyclic pseudo-peptide VQIV(4BF)(ORN)(HAO)KL(ORN)
KeywordsPROTEIN FIBRIL / beta sheet tetramer / beta strand
Function / homologyACETIC ACID
Function and homology information
MethodX-RAY DIFFRACTION / SAD / Resolution: 2.05 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 / chem_comp_atom ...atom_site / 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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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 / _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 VQIV(4BF)(ORN)(HAO)KL(ORN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,5423
Polymers1,3891
Non-polymers1522
Water21612
1
A: Cyclic pseudo-peptide VQIV(4BF)(ORN)(HAO)KL(ORN)
hetero molecules

A: Cyclic pseudo-peptide VQIV(4BF)(ORN)(HAO)KL(ORN)
hetero molecules

A: Cyclic pseudo-peptide VQIV(4BF)(ORN)(HAO)KL(ORN)
hetero molecules

A: Cyclic pseudo-peptide VQIV(4BF)(ORN)(HAO)KL(ORN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,16612
Polymers5,5584
Non-polymers6098
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_635y+3/2,x-3/2,-z+1/21
crystal symmetry operation10_745-x+2,-y-1,z1
crystal symmetry operation16_555-y+1/2,-x+1/2,-z+1/21
Buried area3470 Å2
ΔGint-30 kcal/mol
Surface area3400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.867, 32.867, 55.413
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-13-

HOH

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Components

#1: Protein/peptide Cyclic pseudo-peptide VQIV(4BF)(ORN)(HAO)KL(ORN)


Mass: 1389.458 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: VQIVY segment from Alzheimer's tau displayed on 42-membered macrocycle scaffold
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 2.69 Å3/Da / Density % sol: 54.32 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: Na/K phosphate pH 6.2, 35% (v/v) (+/-)-2-Methyl-2,4-pentanediol, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-D / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 25, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.05→80 Å / Num. obs: 1819 / % possible obs: 98.8 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.046 / Χ2: 0.975 / Net I/σ(I): 26.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.05-2.126.90.1041800.922197.8
2.12-2.216.90.0991750.735197.8
2.21-2.317.10.0881791.352197.8
2.31-2.4370.0811830.947199.5
2.43-2.587.20.0751861.015198.9
2.58-2.787.10.061890.876199
2.78-3.067.20.0541760.942199.4
3.06-3.517.20.041740.944198.3
3.51-4.427.30.0371880.9931100
4.42-807.10.0311891.007199

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
CrystalCleardata collection
DENZOdata reduction
SHELXEmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.05→28.27 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.961 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 6.691 / SU ML: 0.094 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2027 61 5.7 %RANDOM
Rwork0.179 ---
obs0.1804 1068 98.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 63.05 Å2 / Biso mean: 17.8411 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å20 Å20 Å2
2--0.22 Å20 Å2
3----0.45 Å2
Refinement stepCycle: LAST / Resolution: 2.05→28.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms93 0 10 12 115
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.022103
X-RAY DIFFRACTIONr_angle_refined_deg1.3092.375122
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.21555
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.76252
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.6451513
X-RAY DIFFRACTIONr_chiral_restr0.0620.213
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0249
X-RAY DIFFRACTIONr_mcbond_it0.6921.540
X-RAY DIFFRACTIONr_mcangle_it1.13255
X-RAY DIFFRACTIONr_scbond_it2.745363
X-RAY DIFFRACTIONr_scangle_it3.5244.567
LS refinement shellResolution: 2.048→2.101 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.443 3 -
Rwork0.224 71 -
all-74 -
obs--96.1 %
Refinement TLS params.Method: refined / Origin x: 28.8908 Å / Origin y: -19.4552 Å / Origin z: 18.8211 Å
111213212223313233
T0.0219 Å2-0.0104 Å20.0142 Å2-0.0098 Å20.0107 Å2--0.0535 Å2
L0.2897 °20.8297 °20.4296 °2--0.0291 °21.0281 °2--1.2383 °2
S0.0357 Å °-0.0206 Å °-0.0252 Å °0.0214 Å °-0.0636 Å °-0.0989 Å °0.0326 Å °0.0065 Å °0.0279 Å °

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