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- PDB-4nw8: Crystal structure of macrocycles containing Abeta17-23 (LV(PHI)(M... -

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Basic information

Entry
Database: PDB / ID: 4nw8
TitleCrystal structure of macrocycles containing Abeta17-23 (LV(PHI)(MEA)AED) and Abeta30-36 (AIIGL(ORN)V)
ComponentsCyclic hexadecapeptide (ORN)LV(PHI)(MEA)AED(ORN)AIIGL(ORN)V
Keywordsde novo protein / protein binding / beta-sheet / beta-hairpin / amyloid
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SAD / Resolution: 2.02 Å
AuthorsSpencer, R.K. / Li, H. / Nowick, J.S.
CitationJournal: J.Am.Chem.Soc. / Year: 2014
Title: X-ray crystallographic structures of trimers and higher-order oligomeric assemblies of a peptide derived from A beta (17-36).
Authors: Spencer, R.K. / Li, H. / Nowick, J.S.
History
DepositionDec 5, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 2, 2014Provider: repository / Type: Initial release
Revision 1.1May 14, 2014Group: Database references
Revision 1.2Jul 9, 2014Group: Database references
Revision 1.3Nov 22, 2017Group: Advisory / Refinement description / Category: pdbx_validate_polymer_linkage / software
Revision 1.4Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _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: Cyclic hexadecapeptide (ORN)LV(PHI)(MEA)AED(ORN)AIIGL(ORN)V
B: Cyclic hexadecapeptide (ORN)LV(PHI)(MEA)AED(ORN)AIIGL(ORN)V
C: Cyclic hexadecapeptide (ORN)LV(PHI)(MEA)AED(ORN)AIIGL(ORN)V
D: Cyclic hexadecapeptide (ORN)LV(PHI)(MEA)AED(ORN)AIIGL(ORN)V
E: Cyclic hexadecapeptide (ORN)LV(PHI)(MEA)AED(ORN)AIIGL(ORN)V
F: Cyclic hexadecapeptide (ORN)LV(PHI)(MEA)AED(ORN)AIIGL(ORN)V
G: Cyclic hexadecapeptide (ORN)LV(PHI)(MEA)AED(ORN)AIIGL(ORN)V
H: Cyclic hexadecapeptide (ORN)LV(PHI)(MEA)AED(ORN)AIIGL(ORN)V
I: Cyclic hexadecapeptide (ORN)LV(PHI)(MEA)AED(ORN)AIIGL(ORN)V
J: Cyclic hexadecapeptide (ORN)LV(PHI)(MEA)AED(ORN)AIIGL(ORN)V
K: Cyclic hexadecapeptide (ORN)LV(PHI)(MEA)AED(ORN)AIIGL(ORN)V
L: Cyclic hexadecapeptide (ORN)LV(PHI)(MEA)AED(ORN)AIIGL(ORN)V
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,78516
Polymers22,66812
Non-polymers1174
Water3,585199
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.680, 68.680, 93.840
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein/peptide
Cyclic hexadecapeptide (ORN)LV(PHI)(MEA)AED(ORN)AIIGL(ORN)V


Mass: 1889.026 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 199 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.82 Å3/Da / Density % sol: 56.36 %
Crystal growTemperature: 298 K / pH: 7.5
Details: 0.1M HEPES, 29% Jeffamine M-600, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Sep 30, 2013
RadiationMonochromator: VARIMAX VHF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.02→29.74 Å / Num. obs: 16770 / % possible obs: 97.4 % / Observed criterion σ(I): 1 / Redundancy: 7.2 % / Biso Wilson estimate: 25.7 Å2 / Rmerge(I) obs: 0.1246 / Net I/σ(I): 28.82
Reflection shellResolution: 2.02→2.05 Å / % possible all: 38

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Processing

Software
NameVersionClassification
CrystalCleardata collection
AutoSolphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.02→29.74 Å / SU ML: 0.21 / σ(F): 1.36 / Phase error: 23.35 / Stereochemistry target values: ML / Details: THE PHI RESIDUES WERE REFINED AS ANISOTROPIC.
RfactorNum. reflection% reflection
Rfree0.237 1625 9.89 %
Rwork0.195 --
obs0.199 14781 96.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.02→29.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1500 0 4 199 1703
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061524
X-RAY DIFFRACTIONf_angle_d1.0992028
X-RAY DIFFRACTIONf_dihedral_angle_d33.567696
X-RAY DIFFRACTIONf_chiral_restr0.065252
X-RAY DIFFRACTIONf_plane_restr0.003240
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0231-2.05470.2625480.2915512X-RAY DIFFRACTION38
2.0547-2.08830.30871490.25081306X-RAY DIFFRACTION97
2.0883-2.12430.26541400.22661281X-RAY DIFFRACTION100
2.1243-2.1630.26391480.22031335X-RAY DIFFRACTION100
2.163-2.20450.25981490.23051301X-RAY DIFFRACTION99
2.2045-2.24950.26921460.21451320X-RAY DIFFRACTION99
2.2495-2.29840.23451410.21331324X-RAY DIFFRACTION99
2.2984-2.35190.26461420.2061273X-RAY DIFFRACTION99
2.3519-2.41070.24511520.20681329X-RAY DIFFRACTION99
2.4107-2.47580.28791470.22391309X-RAY DIFFRACTION98
2.4758-2.54860.28981350.22231283X-RAY DIFFRACTION99
2.5486-2.63080.2241620.23111328X-RAY DIFFRACTION99
2.6308-2.72480.25571480.22161324X-RAY DIFFRACTION100
2.7248-2.83380.27421460.20981322X-RAY DIFFRACTION100
2.8338-2.96270.23231450.18561328X-RAY DIFFRACTION100
2.9627-3.11870.23941320.20231311X-RAY DIFFRACTION100
3.1187-3.31390.28131440.19421332X-RAY DIFFRACTION100
3.3139-3.56940.21251560.19781307X-RAY DIFFRACTION100
3.5694-3.92780.24541380.16931314X-RAY DIFFRACTION100
3.9278-4.49450.18531440.15391335X-RAY DIFFRACTION100
4.4945-5.65620.17831430.15421323X-RAY DIFFRACTION100
5.6562-29.74250.24471300.20251318X-RAY DIFFRACTION99

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