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- PDB-6vu4: Structure of a beta-hairpin peptide mimic derived from Abeta 14-36 -

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Basic information

Entry
Database: PDB / ID: 6vu4
TitleStructure of a beta-hairpin peptide mimic derived from Abeta 14-36
ComponentsBeta-hairpin Amyloid-beta precursor peptide mimic
KeywordsNEUROPEPTIDE / Alzheimer's disease
Function / homologyIODIDE ION
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.077 Å
AuthorsWierzbicki, M. / Kreutzer, A. / Samdin, T. / Nowick, J.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM097562 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2020
Title: Effects of N-Terminal Residues on the Assembly of Constrained beta-Hairpin Peptides Derived from A beta.
Authors: Samdin, T.D. / Wierzbicki, M. / Kreutzer, A.G. / Howitz, W.J. / Valenzuela, M. / Smith, A. / Sahrai, V. / Truex, N.L. / Klun, M. / Nowick, J.S.
History
DepositionFeb 14, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 15, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Beta-hairpin Amyloid-beta precursor peptide mimic
A: Beta-hairpin Amyloid-beta precursor peptide mimic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,1545
Polymers3,8652
Non-polymers2893
Water64936
1
C: Beta-hairpin Amyloid-beta precursor peptide mimic
A: Beta-hairpin Amyloid-beta precursor peptide mimic
hetero molecules

C: Beta-hairpin Amyloid-beta precursor peptide mimic
A: Beta-hairpin Amyloid-beta precursor peptide mimic
hetero molecules

C: Beta-hairpin Amyloid-beta precursor peptide mimic
A: Beta-hairpin Amyloid-beta precursor peptide mimic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,46215
Polymers11,5956
Non-polymers8689
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation30_566z,-x+3/2,-y+3/21
crystal symmetry operation84_665-y+3/2,-z+3/2,x1
Buried area6000 Å2
ΔGint-42 kcal/mol
Surface area5910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.880, 96.880, 96.880
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number209
Space group name H-MF432
Components on special symmetry positions
IDModelComponents
11A-101-

IOD

21A-102-

CL

31C-212-

HOH

41C-213-

HOH

51C-214-

HOH

61C-215-

HOH

71C-217-

HOH

81A-209-

HOH

91A-212-

HOH

101A-214-

HOH

111A-216-

HOH

121A-217-

HOH

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Components

#1: Protein/peptide Beta-hairpin Amyloid-beta precursor peptide mimic / APP / ABPP / APPI / Alzheimer disease amyloid protein / Amyloid precursor protein / Amyloid-beta A4 ...APP / ABPP / APPI / Alzheimer disease amyloid protein / Amyloid precursor protein / Amyloid-beta A4 protein / Cerebral vascular amyloid peptide / CVAP / PreA4 / Protease nexin-II / PN-II


Mass: 1932.418 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Chemical ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: I
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.45 Å3/Da / Density % sol: 49.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 0.1 M HEPES buffer at pH 7.2, 0.2 M sodium citrate, and 25% isopropanol

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Data collection

DiffractionMean temperature: 170 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN 92 / Detector: CCD / Date: Sep 8, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.077→24.22 Å / Num. obs: 94127 / % possible obs: 100 % / Redundancy: 35.7 % / CC1/2: 0.999 / Net I/σ(I): 22.2
Reflection shellResolution: 2.077→2.16 Å / Num. unique obs: 8323 / CC1/2: 0.914

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260)refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5W4H

5w4h


Resolution: 2.077→24.22 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 33.03
RfactorNum. reflection% reflection
Rfree0.2705 439 9.85 %
Rwork0.2217 --
obs0.2266 4457 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.077→24.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms270 0 3 36 309
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003284
X-RAY DIFFRACTIONf_angle_d1.036377
X-RAY DIFFRACTIONf_dihedral_angle_d22.905204
X-RAY DIFFRACTIONf_chiral_restr0.13745
X-RAY DIFFRACTIONf_plane_restr0.00245
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.077-2.37710.35411460.231324X-RAY DIFFRACTION100
2.3771-2.99410.29911470.24931334X-RAY DIFFRACTION100
2.9941-24.220.24151460.20961360X-RAY DIFFRACTION100

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