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- PDB-6uf7: S2 symmetric peptide design number 5, Uncle Fester -

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Basic information

Entry
Database: PDB / ID: 6uf7
TitleS2 symmetric peptide design number 5, Uncle Fester
ComponentsS2-5, Uncle Fester
KeywordsDE NOVO PROTEIN / cyclic peptide / centrosymmetric macrocycle / L- and D-amino acids
Function / homologypolypeptide(D)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 0.8 Å
Model detailsS2 symmetric cyclic peptide
AuthorsMulligan, V.K. / Kang, C.S. / Antselovich, I. / Sawaya, M.R. / Yeates, T.O. / Baker, D.
Funding support United States, 2items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-FC02-02ER63421 United States
Department of Energy (DOE, United States)DE-AC02-06CH11357 United States
CitationJournal: Protein Sci. / Year: 2020
Title: Computational design of mixed chirality peptide macrocycles with internal symmetry.
Authors: Mulligan, V.K. / Kang, C.S. / Sawaya, M.R. / Rettie, S. / Li, X. / Antselovich, I. / Craven, T.W. / Watkins, A.M. / Labonte, J.W. / DiMaio, F. / Yeates, T.O. / Baker, D.
History
DepositionSep 23, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 2, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: S2-5, Uncle Fester


Theoretical massNumber of molelcules
Total (without water)1,1851
Polymers1,1851
Non-polymers00
Water543
1
A: S2-5, Uncle Fester

A: S2-5, Uncle Fester


Theoretical massNumber of molelcules
Total (without water)2,3712
Polymers2,3712
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_666-x+1,-y+1,-z+11
Unit cell
Length a, b, c (Å)12.200, 10.980, 25.540
Angle α, β, γ (deg.)90.000, 114.903, 90.000
Int Tables number14
Space group name H-MP121/c1
Space group name Hall-P2ybc
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z+1/2
#3: -x,-y,-z
#4: x,-y-1/2,z-1/2

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Components

#1: Polypeptide(D) S2-5, Uncle Fester


Mass: 1185.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: ab initio design / Source: (synth.) synthetic construct (others)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O
Compound detailsThe asymmetric unit contains half of the molecule. The second half is generated by a ...The asymmetric unit contains half of the molecule. The second half is generated by a crystallographic symmetry operator.
Has ligand of interestN
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

Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.17 M ammonium sulfate, 25.5% (w/v) PEG 4000, 15% (v/v) glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.7293 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 22, 2018
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7293 Å / Relative weight: 1
ReflectionResolution: 0.8→11.583 Å / Num. obs: 6184 / % possible obs: 97.1 % / Redundancy: 6.46 % / Biso Wilson estimate: 4.617 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.079 / Rrim(I) all: 0.086 / Χ2: 1.026 / Net I/σ(I): 19.01
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
0.8-0.826.2980.08516.074560.9950.09293.6
0.82-0.846.2670.08315.964090.9950.09191.3
0.84-0.876.1070.08316.344490.990.09198.7
0.87-0.896.5720.07817.734090.9980.08497.1
0.89-0.926.470.08217.794110.9960.08996
0.92-0.966.290.08217.94030.9890.0998.5
0.96-0.996.1350.07318.913840.9960.0897.2
0.99-1.036.7560.08419.283650.9950.0996.6
1.03-1.086.5720.07919.823530.9950.085100
1.08-1.136.5670.07619.933230.9910.08396.7
1.13-1.196.060.07319.653320.9930.08197.1
1.19-1.276.9320.07820.863090.9950.08597.8
1.27-1.356.6780.07620.692920.9920.08399.3
1.35-1.466.6430.0720.42580.9950.077100
1.46-1.66.4840.07320.862460.9910.0895.7
1.6-1.796.6110.07921.992260.9930.08697
1.79-2.076.9390.07722.451980.9940.084100
2.07-2.536.8040.07822.671630.9920.08599.4
2.53-3.586.0690.07821.581300.9920.08697
3.58-11.5836.5740.09322.68680.9790.10197.1

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Processing

Software
NameVersionClassification
XDS20180126data reduction
XSCALE20180126data scaling
PHENIX1.16_3549refinement
PDB_EXTRACT3.25data extraction
SHELXTphasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 0.8→11.58 Å / SU ML: -0 / Cross valid method: FREE R-VALUE / σ(F): 1.47 / Phase error: 3.0849
RfactorNum. reflection% reflection
Rfree0.0518 619 10.01 %
Rwork0.0503 --
obs0.0504 6183 97.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 1.7 Å2
Refinement stepCycle: LAST / Resolution: 0.8→11.58 Å /
ProteinNucleic acidLigandSolventTotal
Num. atoms41 0 0 3 44
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.010341
X-RAY DIFFRACTIONf_angle_d1.702953
X-RAY DIFFRACTIONf_chiral_restr0.09176
X-RAY DIFFRACTIONf_plane_restr0.00676
X-RAY DIFFRACTIONf_dihedral_angle_d45.457418
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.8-0.880.0581510.06111352X-RAY DIFFRACTION95.37
0.88-1.010.05261550.05341402X-RAY DIFFRACTION97.01
1.01-1.270.04491560.04611406X-RAY DIFFRACTION98.36
1.27-11.580.05371570.04831404X-RAY DIFFRACTION98.61

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