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- PDB-7ucp: computationally designed macrocycle -

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Basic information

Entry
Database: PDB / ID: 7ucp
Titlecomputationally designed macrocycle
Componentscomputationally designed cyclic peptide D8.3.p2
KeywordsDE NOVO PROTEIN / D8.3.p2 / cyclic peptide
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 0.85 Å
AuthorsBhardwaj, G. / Baker, D. / Rettie, S. / Glynn, C. / Sawaya, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM124165 United States
CitationJournal: Cell / Year: 2022
Title: Accurate de novo design of membrane-traversing macrocycles.
Authors: Bhardwaj, G. / O'Connor, J. / Rettie, S. / Huang, Y.H. / Ramelot, T.A. / Mulligan, V.K. / Alpkilic, G.G. / Palmer, J. / Bera, A.K. / Bick, M.J. / Di Piazza, M. / Li, X. / Hosseinzadeh, P. / ...Authors: Bhardwaj, G. / O'Connor, J. / Rettie, S. / Huang, Y.H. / Ramelot, T.A. / Mulligan, V.K. / Alpkilic, G.G. / Palmer, J. / Bera, A.K. / Bick, M.J. / Di Piazza, M. / Li, X. / Hosseinzadeh, P. / Craven, T.W. / Tejero, R. / Lauko, A. / Choi, R. / Glynn, C. / Dong, L. / Griffin, R. / van Voorhis, W.C. / Rodriguez, J. / Stewart, L. / Montelione, G.T. / Craik, D. / Baker, D.
History
DepositionMar 17, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 14, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: computationally designed cyclic peptide D8.3.p2


Theoretical massNumber of molelcules
Total (without water)9051
Polymers9051
Non-polymers00
Water181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)10.220, 44.920, 11.560
Angle α, β, γ (deg.)90.000, 102.860, 90.000
Int Tables number14
Space group name H-MP121/c1
Space group name Hall-P2ybc

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Components

#1: Protein/peptide computationally designed cyclic peptide D8.3.p2


Mass: 905.217 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Designed target sequence: Leu Val D-Pro MLE Leu Ile D-Pro MLE Peptide is N to C cyclized.
Source: (synth.) synthetic construct (others)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 1.43 Å3/Da
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 1mg/ml peptide in acetonitrile

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Data collection

DiffractionMean temperature: 196 K / Ambient temp details: LN2 gas / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.8377 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8377 Å / Relative weight: 1
ReflectionResolution: 0.85→100 Å / Num. obs: 8258 / % possible obs: 92.3 % / Redundancy: 4.96 % / Biso Wilson estimate: 47.95 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.049 / Net I/σ(I): 15.63
Reflection shellResolution: 0.85→0.87 Å / Rmerge(I) obs: 0.315 / Mean I/σ(I) obs: 3.08 / Num. unique obs: 364 / CC1/2: 0.942 / % possible all: 56.4

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Processing

Software
NameVersionClassification
PHENIX1.20_4459refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
SHELXTphasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 0.85→22.46 Å / SU ML: 0.0543 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 8.1592
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.1021 824 10.04 %RANDOM
Rwork0.0964 7382 --
obs0.0969 8206 91.91 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 5.82 Å2
Refinement stepCycle: LAST / Resolution: 0.85→22.46 Å /
ProteinNucleic acidLigandSolventTotal
Num. atoms63 0 0 1 64
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123128
X-RAY DIFFRACTIONf_angle_d2.6582176
X-RAY DIFFRACTIONf_chiral_restr0.134424
X-RAY DIFFRACTIONf_plane_restr0.017718
X-RAY DIFFRACTIONf_dihedral_angle_d22.078968
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.85-0.90.31441040.2848926X-RAY DIFFRACTION69.97
0.9-0.970.16081390.17871228X-RAY DIFFRACTION90.89
0.97-1.070.11971440.12011290X-RAY DIFFRACTION96.57
1.07-1.220.08871440.08591297X-RAY DIFFRACTION97.17
1.22-1.540.091470.07811321X-RAY DIFFRACTION98.66
1.54-22.460.07921460.07211320X-RAY DIFFRACTION98.06

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