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- PDB-6ud9: S2 symmetric peptide design number 2, Morticia -

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Basic information

Entry
Database: PDB / ID: 6ud9
TitleS2 symmetric peptide design number 2, Morticia
ComponentsS2-2, Morticia
KeywordsDE NOVO PROTEIN / cyclic peptide / centrosymmetric macrocycle / L and D-amino acids
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.1 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 19, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2020Group: Data collection / Category: reflns_shell / Item: _reflns_shell.percent_possible_all
Revision 1.2Dec 2, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Oct 23, 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

Downloads & links

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Assembly

Deposited unit
A: S2-2, Morticia


Theoretical massNumber of molelcules
Total (without water)9261
Polymers9261
Non-polymers00
Water1629
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)25.690, 11.630, 28.930
Angle α, β, γ (deg.)90.000, 139.577, 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: Protein/peptide S2-2, Morticia


Mass: 926.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O
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

CrystalDensity Matthews: 1.51 Å3/Da / Density % sol: 18.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.1 M potassium thiocyanate, 30% (w/v) PEG 2000 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 2, 2018
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.1→16.7 Å / Num. obs: 3969 / % possible obs: 88.4 % / Redundancy: 6.012 % / Biso Wilson estimate: 10.525 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.055 / Rrim(I) all: 0.061 / Χ2: 1.074 / Net I/σ(I): 21.91
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.1-1.133.9320.089.451470.9940.09342.1
1.13-1.164.5790.0612.661900.9980.06857.6
1.16-1.194.6130.06314.592220.9990.07174
1.19-1.235.5210.07116.112800.9950.07891.2
1.23-1.276.2750.06717.22910.9970.073100
1.27-1.326.1150.06617.062790.9940.07497.6
1.32-1.376.5020.0619.412730.9980.06598.9
1.37-1.426.4790.05919.842570.9980.06496.6
1.42-1.486.0110.05620.532610.9980.06199.2
1.48-1.566.6760.05923.372220.9970.06498.2
1.56-1.646.50.05125.992360.9990.05698.3
1.64-1.746.4360.05326.672180.9980.05799.1
1.74-1.866.3750.04827.171920.9980.05396.5
1.86-2.015.9890.04528.331870.9990.04994.9
2.01-2.26.5440.04530.841710.9980.04999.4
2.2-2.466.5410.05231.51590.9980.05697.5
2.46-2.846.4760.04930.931430.9980.05396.6
2.84-3.486.1170.06130.771030.9950.06794.5
3.48-4.925.9770.06732.12880.9880.07491.7
4.92-16.75.960.06530.59500.9980.07194.3

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Processing

Software
NameVersionClassification
XDS20180126data reduction
XSCALE20180126data scaling
PHENIXv1.16refinement
PDB_EXTRACT3.25data extraction
SHELXDphasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.1→16.66 Å / SU ML: 0.0246 / Cross valid method: FREE R-VALUE / σ(F): 1.44 / Phase error: 12.99
RfactorNum. reflection% reflection
Rfree0.1497 397 10.01 %
Rwork0.1262 --
obs0.1284 3965 89.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 9.71 Å2
Refinement stepCycle: LAST / Resolution: 1.1→16.66 Å /
ProteinNucleic acidLigandSolventTotal
Num. atoms64 0 0 9 73
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012986
X-RAY DIFFRACTIONf_angle_d1.7979116
X-RAY DIFFRACTIONf_chiral_restr0.193313
X-RAY DIFFRACTIONf_plane_restr0.008713
X-RAY DIFFRACTIONf_dihedral_angle_d26.290943
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1-1.260.14131050.1146949X-RAY DIFFRACTION70.93
1.26-1.590.13031470.12471319X-RAY DIFFRACTION99.66
1.59-16.660.16111450.12911300X-RAY DIFFRACTION98.63

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