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- PDB-3t4g: AIIGLMV segment from Alzheimer's Amyloid-Beta displayed on 54-mem... -

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Basic information

Entry
Database: PDB / ID: 3t4g
TitleAIIGLMV segment from Alzheimer's Amyloid-Beta displayed on 54-membered macrocycle scaffold
ComponentsCyclic pseudo-peptide (ORN)AIIGLMV(ORN)KF(HAO)(4BF)K
KeywordsUNKNOWN FUNCTION / amyloid-related / macrocycle / hao
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.7 Å
AuthorsZhao, M. / Liu, C. / Cheng, P.N. / Eisenberg, D. / Nowick, J.S.
CitationJournal: Nat Chem / Year: 2012
Title: Amyloid beta-sheet mimics that antagonize protein aggregation and reduce amyloid toxicity.
Authors: Cheng, P.N. / Liu, C. / Zhao, M. / Eisenberg, D. / Nowick, J.S.
History
DepositionJul 26, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 16, 2014Group: Database references
Revision 1.2Oct 11, 2017Group: Advisory / Data collection / Category: pdbx_validate_polymer_linkage / reflns_shell / Item: _reflns_shell.percent_possible_all
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...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_rmsd_angle / struct_conn / struct_ref_seq / 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_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _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 (ORN)AIIGLMV(ORN)KF(HAO)(4BF)K
B: Cyclic pseudo-peptide (ORN)AIIGLMV(ORN)KF(HAO)(4BF)K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,2137
Polymers3,6222
Non-polymers5915
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Cyclic pseudo-peptide (ORN)AIIGLMV(ORN)KF(HAO)(4BF)K
hetero molecules

A: Cyclic pseudo-peptide (ORN)AIIGLMV(ORN)KF(HAO)(4BF)K
hetero molecules

A: Cyclic pseudo-peptide (ORN)AIIGLMV(ORN)KF(HAO)(4BF)K
hetero molecules

A: Cyclic pseudo-peptide (ORN)AIIGLMV(ORN)KF(HAO)(4BF)K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,19012
Polymers7,2444
Non-polymers9458
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_655-x+1,y,-z1
crystal symmetry operation4_555x,-y,-z1
Buried area2650 Å2
ΔGint-30 kcal/mol
Surface area4750 Å2
MethodPISA
3
A: Cyclic pseudo-peptide (ORN)AIIGLMV(ORN)KF(HAO)(4BF)K
hetero molecules

A: Cyclic pseudo-peptide (ORN)AIIGLMV(ORN)KF(HAO)(4BF)K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,0956
Polymers3,6222
Non-polymers4734
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z1
Buried area680 Å2
ΔGint-6 kcal/mol
Surface area3020 Å2
MethodPISA
4
A: Cyclic pseudo-peptide (ORN)AIIGLMV(ORN)KF(HAO)(4BF)K
B: Cyclic pseudo-peptide (ORN)AIIGLMV(ORN)KF(HAO)(4BF)K
hetero molecules

A: Cyclic pseudo-peptide (ORN)AIIGLMV(ORN)KF(HAO)(4BF)K
B: Cyclic pseudo-peptide (ORN)AIIGLMV(ORN)KF(HAO)(4BF)K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,42614
Polymers7,2444
Non-polymers1,18210
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z1
Buried area2240 Å2
ΔGint-16 kcal/mol
Surface area5310 Å2
MethodPISA
5
B: Cyclic pseudo-peptide (ORN)AIIGLMV(ORN)KF(HAO)(4BF)K
hetero molecules

B: Cyclic pseudo-peptide (ORN)AIIGLMV(ORN)KF(HAO)(4BF)K
hetero molecules

B: Cyclic pseudo-peptide (ORN)AIIGLMV(ORN)KF(HAO)(4BF)K
hetero molecules

B: Cyclic pseudo-peptide (ORN)AIIGLMV(ORN)KF(HAO)(4BF)K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,66216
Polymers7,2444
Non-polymers1,41812
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-x+1,y,-z1
crystal symmetry operation4_565x,-y+1,-z1
Buried area2760 Å2
ΔGint-26 kcal/mol
Surface area4940 Å2
MethodPISA
6
B: Cyclic pseudo-peptide (ORN)AIIGLMV(ORN)KF(HAO)(4BF)K
hetero molecules

B: Cyclic pseudo-peptide (ORN)AIIGLMV(ORN)KF(HAO)(4BF)K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,3318
Polymers3,6222
Non-polymers7096
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z1
Buried area690 Å2
ΔGint-6 kcal/mol
Surface area3160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.390, 44.390, 44.390
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number195
Space group name H-MP23
Detailsbiological unit is the same as asym.

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Components

#1: Protein/peptide Cyclic pseudo-peptide (ORN)AIIGLMV(ORN)KF(HAO)(4BF)K


Mass: 1811.035 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Synthetic construct
#2: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM

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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: 2.01 Å3/Da / Density % sol: 38.88 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 35% (v/v) 2-methyl-2,4-pentanediol, Na/K phosphate buffer pH6.2, pH 7.0, vapor diffusion, hanging drop, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9196, 1.8443
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 4, 2011
RadiationProtocol: SIRAS / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.91961
21.84431
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.503
11L, -K, H20.497
ReflectionHighest resolution: 1.7 Å / Num. obs: 3384 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.035 / Net I/σ(I): 29.74
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.7-1.740.5133.07195.9
1.74-1.790.5473.73199.6
1.79-1.840.3945.581100
1.84-1.90.3157.12199.1
1.9-1.960.2169.791100
1.96-2.030.19211.441100
2.03-2.10.13716.161100
2.1-2.190.10920.4199.5
2.19-2.290.09621.761100
2.29-2.40.1119.871100
2.4-2.530.05637.631100
2.53-2.680.05733.511100
2.68-2.870.04644.381100
2.87-3.10.03359.291100
3.1-3.390.02764.671100
3.39-3.790.0276.62198.4
3.79-4.380.01792.621100
4.38-5.360.01793.461100
5.36-7.580.01687.141100
7.580.01584.59189.8

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: SIRAS / Resolution: 1.7→18.12 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.927 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 4.277 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.035 / ESU R Free: 0.031 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27424 326 9.7 %RANDOM
Rwork0.23629 ---
obs0.24031 3047 99.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.374 Å2
Refinement stepCycle: LAST / Resolution: 1.7→18.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms240 0 40 0 280
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.022295
X-RAY DIFFRACTIONr_bond_other_d0.0040.02214
X-RAY DIFFRACTIONr_angle_refined_deg2.7292.357398
X-RAY DIFFRACTIONr_angle_other_deg1.9013.015493
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.272514
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.373202
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.3341534
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1070.239
X-RAY DIFFRACTIONr_gen_planes_refined0.0260.021254
X-RAY DIFFRACTIONr_gen_planes_other0.0160.02150
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_it2.4131.5126
X-RAY DIFFRACTIONr_mcbond_other0.7441.566
X-RAY DIFFRACTIONr_mcangle_it3.8112207
X-RAY DIFFRACTIONr_scbond_it5.2073169
X-RAY DIFFRACTIONr_scangle_it74.5191
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.699→1.743 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.377 28 -
Rwork0.241 220 -
obs--98.8 %
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)
13.0521.35591.33683.41650.63340.58870.2718-0.02040.1824-0.385-0.32390.01250.13-0.01480.05220.16910.0299-0.00860.07790.01550.045419.09494.6588-4.2862
20.06040.21870.16742.8063-0.10130.81950.02150.00670.08750.0051-0.12940.4090.17510.09470.1080.05380.0027-0.00530.074-0.01620.211317.744817.3045-2.48
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 13
2X-RAY DIFFRACTION2B0 - 13

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