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- PDB-6udr: S2 symmetric peptide design number 3 crystal form 1, Lurch -

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Basic information

Entry
Database: PDB / ID: 6udr
TitleS2 symmetric peptide design number 3 crystal form 1, Lurch
ComponentsS2-3, Lurch crystal form 1
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 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 1.1Dec 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 1.2Nov 13, 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: S2-3, Lurch crystal form 1


Theoretical massNumber of molelcules
Total (without water)1,2151
Polymers1,2151
Non-polymers00
Water724
1
A: S2-3, Lurch crystal form 1

A: S2-3, Lurch crystal form 1


Theoretical massNumber of molelcules
Total (without water)2,4312
Polymers2,4312
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,-z1
Unit cell
Length a, b, c (Å)11.750, 12.930, 12.970
Angle α, β, γ (deg.)104.177, 103.843, 116.298
Int Tables number2
Space group name H-MP-1
Space group name Hall-P1
Symmetry operation#1: x,y,z
#2: -x,-y,-z

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Components

#1: Protein/peptide S2-3, Lurch crystal form 1


Mass: 1215.273 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.: 4 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCrystallographic symmetry operator -x,-y,-z generates the C-terminal half of the cyclic peptide ...Crystallographic symmetry operator -x,-y,-z generates the C-terminal half of the cyclic peptide Q(DTH)(DAR)(DPR)(DAS)
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

CrystalMosaicity: 0 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 1.6 M trisodium citrate, pH 6.5

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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: Mar 22, 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→11.52 Å / Num. obs: 2461 / % possible obs: 75 % / Redundancy: 3.5 % / CC1/2: 0.985 / Rmerge(I) obs: 0.127 / Rpim(I) all: 0.08 / Rrim(I) all: 0.151 / Net I/σ(I): 9.5
Reflection shellResolution: 1.05→1.17 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.145 / Num. measured all: 1742 / Num. unique obs: 515 / CC1/2: 0.961 / Rpim(I) all: 0.095 / Rrim(I) all: 0.175 / Net I/σ(I) obs: 8 / % possible all: 62

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Processing

Software
NameVersionClassification
XDS20180126data reduction
Aimless0.7.1data scaling
PHENIXv1.16refinement
PDB_EXTRACT3.25data extraction
SHELXTphasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1→11.52 Å / SU ML: 0.0451 / Cross valid method: FREE R-VALUE / σ(F): 2.19 / Phase error: 7.6413
RfactorNum. reflection% reflection
Rfree0.0919 246 10 %
Rwork0.0751 --
obs0.0768 2460 75.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 1.44 Å2
Refinement stepCycle: LAST / Resolution: 1→11.52 Å /
ProteinNucleic acidLigandSolventTotal
Num. atoms42 0 0 4 46
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012942
X-RAY DIFFRACTIONf_angle_d1.546856
X-RAY DIFFRACTIONf_chiral_restr0.16146
X-RAY DIFFRACTIONf_plane_restr0.02098
X-RAY DIFFRACTIONf_dihedral_angle_d14.35218
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1-1.260.0932920.0707834X-RAY DIFFRACTION57.2
1.26-11.520.09131540.0771380X-RAY DIFFRACTION93.48

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