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- PDB-5f1t: Crystal structure of a macrocyclic peptide containing fragments f... -

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Basic information

Entry
Database: PDB / ID: 5f1t
TitleCrystal structure of a macrocyclic peptide containing fragments from alpha-synuclein 36-55.
ComponentsMacrocyclic peptide
KeywordsIMMUNE SYSTEM / beta-Hairpins
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.971 Å
AuthorsSalveson, P.J. / Spencer, R.K. / Nowick, J.S.
CitationJournal: J.Am.Chem.Soc. / Year: 2016
Title: X-ray Crystallographic Structure of Oligomers Formed by a Toxic beta-Hairpin Derived from alpha-Synuclein: Trimers and Higher-Order Oligomers.
Authors: Salveson, P.J. / Spencer, R.K. / Nowick, J.S.
History
DepositionNov 30, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2016Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Macrocyclic peptide
B: Macrocyclic peptide
C: Macrocyclic peptide
D: Macrocyclic peptide
E: Macrocyclic peptide
F: Macrocyclic peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,78812
Polymers10,3496
Non-polymers4396
Water1,910106
1
A: Macrocyclic peptide
B: Macrocyclic peptide
C: Macrocyclic peptide
D: Macrocyclic peptide
E: Macrocyclic peptide
F: Macrocyclic peptide
hetero molecules

A: Macrocyclic peptide
B: Macrocyclic peptide
C: Macrocyclic peptide
D: Macrocyclic peptide
E: Macrocyclic peptide
F: Macrocyclic peptide
hetero molecules

A: Macrocyclic peptide
B: Macrocyclic peptide
C: Macrocyclic peptide
D: Macrocyclic peptide
E: Macrocyclic peptide
F: Macrocyclic peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,36336
Polymers31,04618
Non-polymers1,31618
Water32418
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_665-z+3/2,-x+1,y+1/21
crystal symmetry operation10_646-y+1,z-1/2,-x+3/21
Buried area19000 Å2
ΔGint-304 kcal/mol
Surface area12660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.518, 77.518, 77.518
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11B-102-

SO4

21B-102-

SO4

31B-206-

HOH

41C-218-

HOH

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Components

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Protein/peptide , 1 types, 6 molecules ABCDEF

#1: Protein/peptide
Macrocyclic peptide


Mass: 1724.804 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 5 types, 112 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.75 Å3/Da / Density % sol: 67.21 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1 M HEPES (pH 8.0), 0.5 M ammonium sulfate, 34% 2-methyl-2,4-pentanediol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.976 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 6, 2014
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.971→38.76 Å / Num. obs: 11211 / % possible obs: 99.85 % / Redundancy: 5.9 % / Net I/σ(I): 12.38

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementResolution: 1.971→38.759 Å / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.7 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2209 2168 10.28 %
Rwork0.1828 --
obs0.1886 21093 99.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.971→38.759 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms678 0 24 106 808
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011724
X-RAY DIFFRACTIONf_angle_d1.509988
X-RAY DIFFRACTIONf_dihedral_angle_d27.573301
X-RAY DIFFRACTIONf_chiral_restr0.052131
X-RAY DIFFRACTIONf_plane_restr0.006117
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9721-2.0180.29361490.24351250X-RAY DIFFRACTION89
2.018-2.06840.35541460.29561283X-RAY DIFFRACTION89
2.0684-2.12440.23261450.21811223X-RAY DIFFRACTION89
2.1244-2.18680.26971400.21471296X-RAY DIFFRACTION90
2.1868-2.25740.48641430.40331145X-RAY DIFFRACTION82
2.2574-2.3380.22291440.21421277X-RAY DIFFRACTION90
2.338-2.43160.24681560.18681267X-RAY DIFFRACTION89
2.4316-2.54220.21891460.20111261X-RAY DIFFRACTION90
2.5422-2.67610.22161420.18811279X-RAY DIFFRACTION90
2.6761-2.84360.19741440.17391262X-RAY DIFFRACTION90
2.8436-3.06290.20521370.15371290X-RAY DIFFRACTION90
3.0629-3.37060.17721440.12931272X-RAY DIFFRACTION90
3.3706-3.85720.1841360.14731271X-RAY DIFFRACTION90
3.8572-4.85530.14971360.12471266X-RAY DIFFRACTION90
4.8553-27.40930.22691480.19951263X-RAY DIFFRACTION89
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)
13.7917-2.56211.61183.9190.43042.8313-0.00350.19770.2688-0.2087-0.0124-0.311-0.4645-0.1307-0.0040.15830.02340.01550.15520.03290.126241.604638.995365.8939
27.5648-0.5755-2.72893.84012.87777.93960.3875-0.05280.43690.4871-0.15650.1003-0.2889-0.1148-0.15270.1594-0.00990.00850.2160.07760.306530.474636.024770.1365
35.3993.18993.83468.20045.55887.98960.04340.101-0.2843-0.0509-0.13970.31370.2688-0.23390.06240.1041-0.0020.00140.1478-0.01620.112644.872724.252759.2562
43.4184-4.10611.72968.86540.25117.41420.14350.7353-0.0037-0.03870.0539-0.61410.19970.6041-0.17720.2265-0.0224-0.06820.2234-0.02870.250549.183213.039962.6132
57.83014.5675-5.23834.3852-5.80668.08340.1088-0.30820.0475-0.1738-0.2715-0.23180.05090.75930.04070.268-0.08710.00070.2577-0.07720.263646.927515.190453.6692
67.5448-3.65683.48795.6778-2.34967.6873-0.03550.14110.61170.33830.1912-0.2371-0.59870.3576-0.16450.1856-0.09590.06710.2586-0.02610.286729.856930.905478.0309
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN C AND RESID 1:16 )C1 - 16
2X-RAY DIFFRACTION2( CHAIN A AND RESID 1:16 )A1 - 16
3X-RAY DIFFRACTION3( CHAIN B AND RESID 1:16 )B1 - 16
4X-RAY DIFFRACTION4( CHAIN D AND RESID 1:16 )D1 - 16
5X-RAY DIFFRACTION5( CHAIN E AND RESID 1:16 )E1 - 16
6X-RAY DIFFRACTION6( CHAIN F AND RESID 1:16 )F1 - 16

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