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- PDB-6ucx: S2 symmetric peptide design number 1, Wednesday -

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Basic information

Entry
Database: PDB / ID: 6ucx
TitleS2 symmetric peptide design number 1, Wednesday
ComponentsS2-1, Wednesday
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: 0.85 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 18, 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 1.2Jul 28, 2021Group: Refinement description / Category: refine / Item: _refine.ls_percent_reflns_obs

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: S2-1, Wednesday
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,1543
Polymers9261
Non-polymers2282
Water362
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)12.580, 29.810, 15.260
Angle α, β, γ (deg.)90.00, 94.21, 90.00
Int Tables number14
Space group name H-MP121/c1

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Components

#1: Protein/peptide S2-1, Wednesday


Mass: 926.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: ab initio design / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-TFA / trifluoroacetic acid / Trifluoroacetic acid


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


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.54 Å3/Da / Density % sol: 20.17 %
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-C / Wavelength: 0.8856 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 18, 2017
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 0.85→14.9 Å / Num. obs: 7989 / % possible obs: 82.4 % / Redundancy: 6.251 % / Biso Wilson estimate: 7.475 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.04 / Rrim(I) all: 0.044 / Χ2: 1.063 / Net I/σ(I): 22.81
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
0.85-0.872.7240.145.281960.9870.17128
0.87-0.93.6230.146.273180.9890.16343.9
0.9-0.924.360.128.344030.9920.13561.2
0.92-0.955.3610.10211.165340.9950.11377.1
0.95-0.986.6780.09613.55380.9970.10486.8
0.98-1.026.6270.08215.975600.9970.08991.1
1.02-1.066.4380.07317.145520.9980.07991.5
1.06-1.16.8170.05622.635530.9980.06195.7
1.1-1.156.6120.05422.875150.9980.05992.1
1.15-1.26.3950.05124.285010.9970.05598.2
1.2-1.276.9210.05125.64800.9980.05693.4
1.27-1.356.7960.04926.584600.9990.05398.5
1.35-1.446.3850.04527.074100.9980.04994.7
1.44-1.556.8780.04630.434190.9990.0598.1
1.55-1.77.0780.04332.93740.9990.04797.7
1.7-1.96.5280.03836.553350.9990.04196
1.9-2.26.5480.03539.582900.9990.03797.3
2.2-2.696.7630.03740.762530.9990.04100
2.69-3.816.5390.03242.791930.9990.03595.1
3.81-14.97.0570.03445.7210510.036100

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Processing

Software
NameVersionClassification
SHELXT2018/3refinement
XDS20170601data reduction
XSCALE20170601data scaling
PDB_EXTRACT3.25data extraction
SHELXTphasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 0.85→14.9 Å / Num. restraintsaints: 1426 / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.085 799 10 %RANDOM
Rwork0.0762 ---
obs-7989 80 %-
Refinement stepCycle: 1 / Resolution: 0.85→14.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms64 0 14 2 80
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.02
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes
X-RAY DIFFRACTIONs_zero_chiral_vol0.137
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.11
X-RAY DIFFRACTIONs_anti_bump_dis_restr
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt
X-RAY DIFFRACTIONs_approx_iso_adps
LS refinement shellResolution: 0.85→0.92 Å /
RfactorNum. reflection
obs0.15 728

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