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- PDB-4ntp: Crystal structure of macrocycles containing A 17-23 (LV(PHI)FAED)... -

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Basic information

Entry
Database: PDB / ID: 4ntp
TitleCrystal structure of macrocycles containing A 17-23 (LV(PHI)FAED) and A 30-36 (AII(SAR)L(ORN)V)
ComponentsCyclic hexadecapeptide (ORN)LV(PHI)FAED(ORN)AII(SAR)L(ORN)V
Keywordsde novo protein / protein binding / beta-sheet / beta-hairpin / amyloid / Phe19 changed to p-iodo-phenylalanine
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.987 Å
AuthorsNowick, J.S. / Spencer, R.K. / Li, H.
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 2, 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 1.3Oct 21, 2020Group: Advisory / Data collection / Derived calculations
Category: pdbx_validate_polymer_linkage / reflns_shell ...pdbx_validate_polymer_linkage / reflns_shell / struct_conn / struct_site
Item: _reflns_shell.Rmerge_I_obs / _reflns_shell.number_unique_all ..._reflns_shell.Rmerge_I_obs / _reflns_shell.number_unique_all / _reflns_shell.number_unique_obs / _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

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Assembly

Deposited unit
A: Cyclic hexadecapeptide (ORN)LV(PHI)FAED(ORN)AII(SAR)L(ORN)V
B: Cyclic hexadecapeptide (ORN)LV(PHI)FAED(ORN)AII(SAR)L(ORN)V
C: Cyclic hexadecapeptide (ORN)LV(PHI)FAED(ORN)AII(SAR)L(ORN)V
D: Cyclic hexadecapeptide (ORN)LV(PHI)FAED(ORN)AII(SAR)L(ORN)V
E: Cyclic hexadecapeptide (ORN)LV(PHI)FAED(ORN)AII(SAR)L(ORN)V
F: Cyclic hexadecapeptide (ORN)LV(PHI)FAED(ORN)AII(SAR)L(ORN)V
G: Cyclic hexadecapeptide (ORN)LV(PHI)FAED(ORN)AII(SAR)L(ORN)V
H: Cyclic hexadecapeptide (ORN)LV(PHI)FAED(ORN)AII(SAR)L(ORN)V
I: Cyclic hexadecapeptide (ORN)LV(PHI)FAED(ORN)AII(SAR)L(ORN)V
J: Cyclic hexadecapeptide (ORN)LV(PHI)FAED(ORN)AII(SAR)L(ORN)V
K: Cyclic hexadecapeptide (ORN)LV(PHI)FAED(ORN)AII(SAR)L(ORN)V
L: Cyclic hexadecapeptide (ORN)LV(PHI)FAED(ORN)AII(SAR)L(ORN)V
M: Cyclic hexadecapeptide (ORN)LV(PHI)FAED(ORN)AII(SAR)L(ORN)V
N: Cyclic hexadecapeptide (ORN)LV(PHI)FAED(ORN)AII(SAR)L(ORN)V
O: Cyclic hexadecapeptide (ORN)LV(PHI)FAED(ORN)AII(SAR)L(ORN)V
P: Cyclic hexadecapeptide (ORN)LV(PHI)FAED(ORN)AII(SAR)L(ORN)V
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,44823
Polymers30,22416
Non-polymers2237
Water5,170287
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.180, 68.180, 170.430
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11E-216-

HOH

21E-219-

HOH

31H-215-

HOH

41H-216-

HOH

51H-218-

HOH

61O-117-

HOH

71O-122-

HOH

DetailsTrimer occurs along a 3-fold axis perpendicular to the β-sheets. / Two trimer units associate along the 3-fold axis / Four timer units associate along the trimer apex.

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Components

#1: Protein/peptide
Cyclic hexadecapeptide (ORN)LV(PHI)FAED(ORN)AII(SAR)L(ORN)V


Mass: 1889.025 Da / Num. of mol.: 16 / Source method: obtained synthetically / 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 / Chloride


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 287 / 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: 2.52 Å3/Da / Density % sol: 51.23 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 25% Jeffamine M-600, 0.1 M HEPES, pH 6.5, 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 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Sep 12, 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: 1.987→34.09 Å / Num. all: 20197 / Num. obs: 20197 / % possible obs: 99.11 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2 / Biso Wilson estimate: 23.13 Å2 / Rmerge(I) obs: 0.1366 / Rsym value: 0.139 / Net I/σ(I): 22.24
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. unique obsDiffraction-ID% possible all
1.987-2.040.4852.23054178.5
2.04-2.090.4063.6629141100
2.09-2.160.364.4929161100
2.16-2.220.3295.3926821100
2.22-2.290.316627291100
2.29-2.370.2517.6426101100

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8.4_1496)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.987→34.09 Å / Isotropic thermal model: Isotropic / σ(F): 1.97 / Phase error: 28.99 / Stereochemistry target values: ML / Details: Phe-I residues were refined as anisotropic
RfactorNum. reflection% reflectionSelection details
Rfree0.2461 1996 4.98 %XDS 5%
Rwork0.2068 ---
obs0.209 18823 98.25 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.987→34.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2000 0 7 287 2294
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062032
X-RAY DIFFRACTIONf_angle_d1.2232720
X-RAY DIFFRACTIONf_dihedral_angle_d32.15960
X-RAY DIFFRACTIONf_chiral_restr0.043336
X-RAY DIFFRACTIONf_plane_restr0.006335
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.987-2.03660.2471260.23562159X-RAY DIFFRACTION78
2.0366-2.09170.22061420.22292712X-RAY DIFFRACTION100
2.0917-2.15320.28431340.22282802X-RAY DIFFRACTION100
2.1532-2.22270.27211360.22012762X-RAY DIFFRACTION100
2.2227-2.30220.27741500.22292771X-RAY DIFFRACTION100
2.3022-2.39430.30211520.22632724X-RAY DIFFRACTION100
2.3943-2.50330.3151540.2332752X-RAY DIFFRACTION100
2.5033-2.63520.3141360.23442818X-RAY DIFFRACTION100
2.6352-2.80020.27381340.23352746X-RAY DIFFRACTION100
2.8002-3.01630.31311440.21082778X-RAY DIFFRACTION100
3.0163-3.31960.23791340.20812750X-RAY DIFFRACTION100
3.3196-3.79940.21061600.19472776X-RAY DIFFRACTION100
3.7994-4.78480.18961200.16362786X-RAY DIFFRACTION100
4.7848-34.0950.22991740.20682709X-RAY DIFFRACTION99

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