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- PDB-6ug2: C2 symmetric peptide design number 1, Zappy, crystal form 2 -

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Basic information

Entry
Database: PDB / ID: 6ug2
TitleC2 symmetric peptide design number 1, Zappy, crystal form 2
ComponentsC2-1, Zappy, crystal form 2
KeywordsDE NOVO PROTEIN / cyclic peptide / 2-fold symmetric / 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 25, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 2, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 2, 2025Group: 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: C2-1, Zappy, crystal form 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,0612
Polymers1,0211
Non-polymers401
Water27015
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)9.810, 17.050, 20.590
Angle α, β, γ (deg.)105.16, 92.17, 105.93
Int Tables number2
Space group name H-MP-1
Symmetry operation#1: x,y,z
#2: -x,-y,-z

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Components

#1: Protein/peptide C2-1, Zappy, crystal form 2


Mass: 1021.079 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Residue 1 is partially racemized. Both DSN and SER are present at this position. The racemization was an undesired side product of the peptide synthesis.
Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O
Compound detailsResidue 1 is partially racemized. Both DSN and SER are present at this position. The racemization ...Residue 1 is partially racemized. Both DSN and SER are present at this position. The racemization was an undesired side product of the peptide synthesis.
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: 1.55 Å3/Da / Density % sol: 20.86 %
Description: needle, 200 microns long and less than 5 microns thick
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2 M calcium chloride, 0.1 M HEPES, pH 7.5, 28% (w/v) PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 14, 2019
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.1→19.734 Å / Num. obs: 4357 / % possible obs: 87.4 % / Redundancy: 4.753 % / Biso Wilson estimate: 11.43 Å2 / Rmerge(I) obs: 0.25 / Net I/σ(I): 4.08
Reflection shellResolution: 1.1→1.13 Å / Redundancy: 4.06 % / Rmerge(I) obs: 0.898 / Mean I/σ(I) obs: 1.14 / Num. unique obs: 240 / % possible all: 66.9

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Processing

Software
NameVersionClassification
PHENIXV1.16-3549refinement
XDS20180808data reduction
XSCALE20180808data scaling
PDB_EXTRACT3.25data extraction
SHELXDphasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.1→19.73 Å / SU ML: 0.077 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.01
RfactorNum. reflection% reflection
Rfree0.182 435 9.99 %
Rwork0.151 --
obs0.154 4353 87.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 11.18 Å2
Refinement stepCycle: LAST / Resolution: 1.1→19.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms76 0 1 15 92
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.017101
X-RAY DIFFRACTIONf_angle_d3.495144
X-RAY DIFFRACTIONf_dihedral_angle_d28.55740
X-RAY DIFFRACTIONf_chiral_restr1.58718
X-RAY DIFFRACTIONf_plane_restr0.02316
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1-1.260.3121270.2651149X-RAY DIFFRACTION77
1.26-1.590.22371500.18941355X-RAY DIFFRACTION90
1.59-19.730.14521580.11671414X-RAY DIFFRACTION95

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