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- PDB-5f1w: Crystal structure of the enantiomer of a macrocyclic peptide cont... -

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Basic information

Entry
Database: PDB / ID: 5f1w
TitleCrystal structure of the enantiomer of a macrocyclic peptide containing fragments from alpha synuclein 36-55
ComponentsMacrocyclic peptide
KeywordsIMMUNE SYSTEM / beta-Hairpins
Function / homologypolypeptide(D) / polypeptide(D) (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.161 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
Revision 1.2Sep 27, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_struct_oper_list / pdbx_validate_polymer_linkage / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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)10,6819
Polymers10,3496
Non-polymers3323
Water99155
1
A: Macrocyclic peptide
C: Macrocyclic peptide
F: Macrocyclic peptide
hetero molecules

A: Macrocyclic peptide
C: Macrocyclic peptide
F: Macrocyclic peptide
hetero molecules

A: Macrocyclic peptide
C: Macrocyclic peptide
F: Macrocyclic peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,87812
Polymers15,5239
Non-polymers3553
Water1629
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area7980 Å2
ΔGint-73 kcal/mol
Surface area7120 Å2
MethodPISA
2
B: Macrocyclic peptide
D: Macrocyclic peptide
E: Macrocyclic peptide
hetero molecules

B: Macrocyclic peptide
D: Macrocyclic peptide
E: Macrocyclic peptide
hetero molecules

B: Macrocyclic peptide
D: Macrocyclic peptide
E: Macrocyclic peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,16615
Polymers15,5239
Non-polymers6436
Water1629
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area8460 Å2
ΔGint-132 kcal/mol
Surface area7220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.910, 77.910, 77.910
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-101-

SO4

21B-101-

SO4

31C-203-

HOH

41C-206-

HOH

51C-207-

HOH

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Components

#1: Polypeptide(D)
Macrocyclic peptide


Mass: 1724.804 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / 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: 3.81 Å3/Da / Density % sol: 67.7 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1 M HEPES (pH 8.0), 0.5 m ammonium sulphate, 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: 0.997 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 2, 2015
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.997 Å / Relative weight: 1
ReflectionResolution: 2.161→34.842 Å / Num. obs: 8669 / % possible obs: 100 % / Redundancy: 2 % / Net I/σ(I): 5.84

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5F1T

5f1t


Resolution: 2.161→34.842 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2828 856 9.87 %
Rwork0.2232 --
obs0.2291 8669 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.161→34.842 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms678 0 21 55 754
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005708
X-RAY DIFFRACTIONf_angle_d1.058962
X-RAY DIFFRACTIONf_dihedral_angle_d32.128294
X-RAY DIFFRACTIONf_chiral_restr0.068128
X-RAY DIFFRACTIONf_plane_restr0.005114
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1608-2.29620.34031400.28561289X-RAY DIFFRACTION100
2.2962-2.47340.30391390.23551260X-RAY DIFFRACTION100
2.4734-2.72230.30371410.24321297X-RAY DIFFRACTION100
2.7223-3.1160.25861400.20081313X-RAY DIFFRACTION100
3.116-3.92490.24181460.19531298X-RAY DIFFRACTION100
3.9249-34.84690.31500.23131364X-RAY DIFFRACTION100
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)
18.3612-1.46382.93056.46292.52426.0897-0.0787-0.3499-0.33051.2088-0.3626-0.49490.211-0.80380.07440.41510.0193-0.05330.36520.05210.39878.6002-2.2989-7.6665
24.5032-0.6699-3.95855.34923.84515.349-0.57470.1132-0.71570.8580.3217-0.37190.92660.09880.24960.30680.0052-0.01030.2655-0.05950.2668-5.8968-14.193-18.2988
34.85155.64130.14527.8739-1.66283.7486-0.1491-0.39750.5856-0.22270.33211.9635-1.33490.2945-0.07510.4076-0.03660.03450.3086-0.0160.294-2.9140.6126-11.5015
48.89073.79254.18534.16821.88757.6702-0.67481.0571-0.30210.1169-0.248-0.2546-0.4939-0.96070.28630.34880.14070.03440.4636-0.12430.3887-10.1328-25.7264-14.9928
52.5727-3.6813.13217.0875-4.59685.94460.3180.07710.2366-0.8098-0.32990.60050.7857-0.47090.03520.320.1199-0.01460.3144-0.13080.3548-7.9887-23.0214-24.1582
63.52292.1755-4.12216.9119-4.64636.3043-0.0138-0.16951.30010.59960.3599-0.3236-0.24820.3057-0.06740.20220.0601-0.10190.4622-0.02240.42889.7886-8.08130.7239
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 16 )
2X-RAY DIFFRACTION2chain 'B' and (resid 1 through 16 )
3X-RAY DIFFRACTION3chain 'C' and (resid 1 through 16)
4X-RAY DIFFRACTION4chain 'D' and (resid 1 through 16 )
5X-RAY DIFFRACTION5chain 'E' and (resid 1 through 16 )
6X-RAY DIFFRACTION6chain 'F' and (resid 1 through 16 )

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