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- PDB-6udz: S2 symmetric peptide design number 4 crystal form 1, Pugsley -

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Basic information

Entry
Database: PDB / ID: 6udz
TitleS2 symmetric peptide design number 4 crystal form 1, Pugsley
ComponentsS2-4, Pusgley crystal form 1
KeywordsDE NOVO PROTEIN / cyclic peptide / centrosymmetric macrocycle / L and D-amino acids
Function / homologytrifluoroacetic acid
Function and homology information
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 20, 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 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
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: S2-4, Pusgley crystal form 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,3483
Polymers1,1201
Non-polymers2282
Water724
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)10.850, 15.020, 21.620
Angle α, β, γ (deg.)100.45, 101.68, 110.55
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 S2-4, Pusgley crystal form 1


Mass: 1120.316 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-TFA / trifluoroacetic acid


Mass: 114.023 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2HF3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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 / pH: 5 / Details: 3.2 M ammonium sulfate, 0.1 M citrate, pH 5.0

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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: 1.1→20.4 Å / Num. obs: 4083 / % possible obs: 83.6 % / Redundancy: 3.308 % / Biso Wilson estimate: 6.65 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.064 / Rrim(I) all: 0.076 / Χ2: 0.997 / Net I/σ(I): 11.51
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.1-1.132.9920.0638.142460.9940.07767.8
1.13-1.163.3370.0519.752790.9960.0679.3
1.16-1.193.2190.0599.322740.9960.0779.9
1.19-1.233.2530.05510.182610.9950.06680.6
1.23-1.273.3040.05310.112800.9960.06484.8
1.27-1.323.1970.0579.982390.9960.06981
1.32-1.373.2950.05111.052710.9970.0681.6
1.37-1.423.5350.05710.932300.9940.06787.5
1.42-1.483.3610.0511.152440.9980.05985.3
1.48-1.563.4280.05212.482220.9960.06181.3
1.56-1.643.3850.05911.362130.9950.06988
1.64-1.743.2330.06212.062020.9940.07287.1
1.74-1.863.3090.05313.232170.9980.06288.6
1.86-2.013.4840.05913.771840.9960.06889.3
2.01-2.23.4890.06214.361820.9920.07391
2.2-2.463.4130.07414.741430.9890.08792.3
2.46-2.843.3780.06614.951430.9910.07988.8
2.84-3.483.1770.0815.231130.9860.09890.4
3.48-4.923.1050.10514.49950.9710.13194.1
4.92-20.43.1110.07314.29450.9840.09277.6

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Processing

Software
NameVersionClassification
PHENIXV1.16refinement
XDS20180126data reduction
XSCALE20180126data scaling
PDB_EXTRACT3.25data extraction
SHELXD2013/2phasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.1→20.36 Å / SU ML: 0.055 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 33.45
RfactorNum. reflection% reflection
Rfree0.149 405 9.97 %
Rwork0.136 --
obs0.137 4061 83.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 4.34 Å2
Refinement stepCycle: LAST / Resolution: 1.1→20.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms78 0 14 4 96
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014107
X-RAY DIFFRACTIONf_angle_d2.139149
X-RAY DIFFRACTIONf_dihedral_angle_d19.74751
X-RAY DIFFRACTIONf_chiral_restr0.07116
X-RAY DIFFRACTIONf_plane_restr0.01117
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1-1.260.1461260.1181149X-RAY DIFFRACTION78
1.26-1.590.13061350.11931216X-RAY DIFFRACTION83
1.59-20.360.15951440.15151291X-RAY DIFFRACTION88

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