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- PDB-6uf4: S2 symmetric peptide design number 4 crystal form 2, Pugsley -

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Basic information

Entry
Database: PDB / ID: 6uf4
TitleS2 symmetric peptide design number 4 crystal form 2, Pugsley
ComponentsS2-4, Pusgley crystal form 2
KeywordsDE NOVO PROTEIN / cyclic peptide / centrosymmetric macrocycle / L and D-amino acids
Function / homologypolypeptide(D)
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 23, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 2, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 23, 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: S2-4, Pusgley crystal form 2
B: S2-4, Pusgley crystal form 2


Theoretical massNumber of molelcules
Total (without water)2,2412
Polymers2,2412
Non-polymers00
Water30617
1
A: S2-4, Pusgley crystal form 2

A: S2-4, Pusgley crystal form 2


Theoretical massNumber of molelcules
Total (without water)2,2412
Polymers2,2412
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,-z1
2
B: S2-4, Pusgley crystal form 2

B: S2-4, Pusgley crystal form 2


  • defined by author
  • 2.24 kDa, 2 polymers
Theoretical massNumber of molelcules
Total (without water)2,2412
Polymers2,2412
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,-z1
Unit cell
Length a, b, c (Å)14.150, 16.410, 16.560
Angle α, β, γ (deg.)102.310, 106.340, 86.240
Int Tables number2
Space group name H-MP-1

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Components

#1: Polypeptide(D) S2-4, Pusgley crystal form 2


Mass: 1120.316 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: ab initio design / Source: (synth.) synthetic construct (others)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O
Compound detailsThe asymmetric unit contains half of the molecule. The second half is generated by a ...The asymmetric unit contains half of the molecule. The second half is generated by a crystallographic symmetry operator.
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: 1.58 Å3/Da / Density % sol: 22.25 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 2.4 M sodium malonate

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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: Mar 22, 2018
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→16.033 Å / Num. obs: 5355 / % possible obs: 94.3 % / Redundancy: 5.815 % / Biso Wilson estimate: 0.68 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.059 / Rrim(I) all: 0.065 / Χ2: 0.992 / Net I/σ(I): 19.14 / Num. measured all: 31141 / Scaling rejects: 200
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.1-1.134.8910.04815.053500.9980.05490
1.13-1.165.870.05174310.9980.05599.3
1.16-1.196.0520.05118.73810.9980.05697.9
1.19-1.235.9240.05218.553970.9980.057100
1.23-1.276.1230.05218.573730.9980.05798.9
1.27-1.315.840.05518.033560.9980.0699.4
1.31-1.366.1820.05419.663520.9970.059100
1.36-1.426.3310.05420.333380.9950.05998.3
1.42-1.486.4210.0620.363160.9960.066100
1.48-1.566.4070.05721.352950.9970.06299.7
1.56-1.646.2730.06220.343110.9960.06899
1.64-1.745.6790.06219.732650.9960.06997.1
1.74-1.865.7590.07120.922570.9920.0895.9
1.86-2.015.8190.07321.292320.9870.08395.9
2.01-2.25.2910.07419.781790.9920.08486.1
2.2-2.465.4010.07221.411770.9880.08283.1
2.46-2.844.7750.06819.661420.9910.07776.3
2.84-3.483.6350.08316.88960.9740.09967.1
3.48-4.924.0570.09118.37700.9780.10658.3
4.92-16.0333.8650.10616.7370.9740.12358.7

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Processing

Software
NameVersionClassification
XDS20180126data reduction
XSCALE20180126data scaling
PHENIX1.16_3549refinement
PDB_EXTRACT3.25data extraction
SHELXDphasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.1→16.033 Å / SU ML: 0.04 / Cross valid method: THROUGHOUT / σ(F): 1.63 / Phase error: 5.41
RfactorNum. reflection% reflection
Rfree0.1014 534 10.02 %
Rwork0.0869 --
obs0.0882 5329 94.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 6.5 Å2 / Biso mean: 1.178 Å2 / Biso min: 0.05 Å2
Refinement stepCycle: final / Resolution: 1.1→16.033 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms78 0 192 44 314
Biso mean--0.88 2.32 -
Num. residues----0
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.1001-1.21070.09181360.0661121897
1.2107-1.38580.08561420.06871284100
1.3858-1.74570.09411400.0794125999
1.7457-16.0330.13041160.1298103481

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