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- PDB-4q8d: Crystal structure of a macrocyclic beta-sheet peptide containing ... -

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Basic information

Entry
Database: PDB / ID: 4q8d
TitleCrystal structure of a macrocyclic beta-sheet peptide containing two beta-strands from amyloid beta residues 15-23
Componentsmacrocyclic beta-sheet peptide incorporating residues amyloid beta 15-23
KeywordsDE NOVO PROTEIN / beta-sheet / synthetic peptide / artificial macrocycle
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.746 Å
AuthorsPham, J.D. / Spencer, R.K. / Chen, K.H. / Nowick, J.S.
CitationJournal: J.Am.Chem.Soc. / Year: 2014
Title: A Fibril-Like Assembly of Oligomers of a Peptide Derived from beta-Amyloid.
Authors: Pham, J.D. / Spencer, R.K. / Chen, K.H. / Nowick, J.S.
History
DepositionApr 26, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 13, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 24, 2014Group: Database references
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.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site.type_symbol / _atom_site_anisotrop.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: macrocyclic beta-sheet peptide incorporating residues amyloid beta 15-23
B: macrocyclic beta-sheet peptide incorporating residues amyloid beta 15-23
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,0374
Polymers4,8012
Non-polymers2362
Water77543
1
A: macrocyclic beta-sheet peptide incorporating residues amyloid beta 15-23
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,5192
Polymers2,4001
Non-polymers1181
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: macrocyclic beta-sheet peptide incorporating residues amyloid beta 15-23
hetero molecules


  • defined by author
  • 2.52 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)2,5192
Polymers2,4001
Non-polymers1181
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: macrocyclic beta-sheet peptide incorporating residues amyloid beta 15-23
hetero molecules

B: macrocyclic beta-sheet peptide incorporating residues amyloid beta 15-23
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,0374
Polymers4,8012
Non-polymers2362
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area1030 Å2
ΔGint-23 kcal/mol
Surface area3910 Å2
MethodPISA
4
A: macrocyclic beta-sheet peptide incorporating residues amyloid beta 15-23
hetero molecules

A: macrocyclic beta-sheet peptide incorporating residues amyloid beta 15-23
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,0374
Polymers4,8012
Non-polymers2362
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area940 Å2
ΔGint-23 kcal/mol
Surface area4150 Å2
MethodPISA
5


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1120 Å2
ΔGint-11 kcal/mol
Surface area3890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.174, 62.852, 20.094
Angle α, β, γ (deg.)90.00, 89.98, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-207-

HOH

21A-224-

HOH

31B-206-

HOH

41B-216-

HOH

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Components

#1: Protein/peptide macrocyclic beta-sheet peptide incorporating residues amyloid beta 15-23


Mass: 2400.423 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.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Water ChemComp-HOH / 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: 2.1 Å3/Da / Density % sol: 41.53 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: 0.1 M sodium citrate, 0.1 M ammonium acetate, 30% 2-methyl-2,4-pentanediol, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.634→31.375 Å / % possible obs: 99.7 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.059
Reflection shellResolution: 1.63→1.7 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.138 / Mean I/σ(I) obs: 9.9 / Num. unique all: 305 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALAdata scaling
SOLVE2.15phasing
RESOLVE2.15phasing
PHENIX1.9_1692refinement
RefinementMethod to determine structure: SAD / Resolution: 1.746→17.557 Å / σ(F): 1.36 / Phase error: 26.68 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2197 812 10.41 %
Rwork0.1794 --
obs0.1862 7802 97.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.746→17.557 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms322 0 16 43 381
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009342
X-RAY DIFFRACTIONf_angle_d1.512456
X-RAY DIFFRACTIONf_dihedral_angle_d28.809170
X-RAY DIFFRACTIONf_chiral_restr0.04644
X-RAY DIFFRACTIONf_plane_restr0.00758
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7489-1.85830.23681370.25891194X-RAY DIFFRACTION88
1.8583-2.00160.27441380.22181169X-RAY DIFFRACTION88
2.0016-2.20260.24311300.20161152X-RAY DIFFRACTION88
2.2026-2.52040.2711350.19781194X-RAY DIFFRACTION88
2.5204-3.17210.21321370.16491135X-RAY DIFFRACTION86
3.1721-16.92990.18031230.14031139X-RAY DIFFRACTION87
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)
10.8739-0.1773-0.12120.8803-0.00940.06480.00610.0280.1026-0.01130.02440.23320.0114-0.0216-0.05420.1080.0883-0.01430.15610.00020.10699.315133.929-1.2276
20.19320.2004-0.31733.1622-1.4450.943-0.0574-0.00420.03080.0277-0.1035-0.0818-0.0292-0.12840.14620.1068-0.0429-0.05230.16530.00380.099810.193519.89991.5058
30.15180.16120.04490.1770.05420.0214-0.002-0.1230.10520.0144-0.02820.0680.019-0.07820.01870.0493-0.0459-0.03060.15250.01680.09559.327920.101211.4177
40.76530.00380.40350.5384-0.58851.31540.0081-0.08350.1205-0.0392-0.0080.0448-0.0164-0.2024-0.00110.13170.07430.01670.15080.00070.061610.464934.22528.5517
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 7 )
2X-RAY DIFFRACTION2chain 'A' and (resid 9 through 18 )
3X-RAY DIFFRACTION3chain 'B' and (resid 1 through 7 )
4X-RAY DIFFRACTION4chain 'B' and (resid 9 through 18 )

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