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- PDB-4yxx: Computationally designed left-handed alpha/alpha toroid with 6 repeats -

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Basic information

Entry
Database: PDB / ID: 4yxx
TitleComputationally designed left-handed alpha/alpha toroid with 6 repeats
ComponentsdTor_6x35L
KeywordsDE NOVO PROTEIN / Rosetta / toroid / alpha helix / computationally designed / left-handed
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.18 Å
AuthorsDoyle, L. / Bolduc, J. / Stoddard, B.L. / Bradley, P.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM49857 United States
CitationJournal: Nature / Year: 2015
Title: Rational design of alpha-helical tandem repeat proteins with closed architectures.
Authors: Doyle, L. / Hallinan, J. / Bolduc, J. / Parmeggiani, F. / Baker, D. / Stoddard, B.L. / Bradley, P.
History
DepositionMar 23, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 30, 2015Group: Database references
Revision 1.2Jan 6, 2016Group: Database references
Revision 1.3Sep 6, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Nov 22, 2017Group: Refinement description / Category: software
Revision 1.5Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: dTor_6x35L


Theoretical massNumber of molelcules
Total (without water)23,7631
Polymers23,7631
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.460, 85.048, 80.464
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein dTor_6x35L


Mass: 23763.473 Da / Num. of mol.: 1 / Fragment: dTor_6x35L / Source method: obtained synthetically / Details: Rosetta designed / Source: (synth.) synthetic construct (others)

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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: 2.28 Å3/Da / Density % sol: 46.16 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1 M Tris, 0.14 M NaCl, 22% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 12, 2013
RadiationMonochromator: Double-crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.18→50 Å / Num. obs: 11706 / % possible obs: 99.7 % / Redundancy: 13.7 % / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.016 / Rrim(I) all: 0.061 / Χ2: 1.047 / Net I/av σ(I): 29.719 / Net I/σ(I): 25.7 / Num. measured all: 160852
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.18-2.2611.60.32311340.9720.0960.3381.35999.2
2.26-2.3513.90.27211630.9850.0740.2821.139100
2.35-2.46140.19511410.9910.0530.2021.006100
2.46-2.5814.20.16511610.9940.0450.1711.142100
2.58-2.7514.20.11711700.9960.0320.1220.987100
2.75-2.9614.30.09211520.9970.0250.0960.971100
2.96-3.2614.30.07411740.9990.020.0760.974100
3.26-3.7314.20.05711750.9990.0160.061.064100
3.73-4.713.80.05111960.9990.0140.0530.99599.8
4.7-5012.80.04112400.9990.0120.0430.998.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Computationally designed model

Resolution: 2.18→43.03 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.906 / WRfactor Rfree: 0.3446 / WRfactor Rwork: 0.2791 / FOM work R set: 0.7461 / SU B: 8.163 / SU ML: 0.206 / SU R Cruickshank DPI: 0.2798 / SU Rfree: 0.2384 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.28 / ESU R Free: 0.238 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2955 553 4.7 %RANDOM
Rwork0.2377 ---
obs0.2403 11137 99.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 118.83 Å2 / Biso mean: 52.459 Å2 / Biso min: 27.79 Å2
Baniso -1Baniso -2Baniso -3
1--0.23 Å20 Å20 Å2
2--2.32 Å20 Å2
3----2.09 Å2
Refinement stepCycle: final / Resolution: 2.18→43.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1476 0 0 0 1476
Num. residues----208
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0191475
X-RAY DIFFRACTIONr_bond_other_d0.0020.021637
X-RAY DIFFRACTIONr_angle_refined_deg1.6912.0312001
X-RAY DIFFRACTIONr_angle_other_deg0.77933703
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1415207
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.46826.47134
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.81715284
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.11156
X-RAY DIFFRACTIONr_chiral_restr0.0850.2286
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021603
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02243
LS refinement shellResolution: 2.177→2.234 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.415 37 -
Rwork0.286 795 -
all-832 -
obs--96.97 %

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