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- PDB-5oos: Designed Ankyrin Repeat Protein (DARPin) YTRL-2 selected by direc... -

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Basic information

Entry
Database: PDB / ID: 5oos
TitleDesigned Ankyrin Repeat Protein (DARPin) YTRL-2 selected by directed evolution against Lysozyme
ComponentsDARPin YTRL-2
KeywordsDE NOVO PROTEIN / DARPin / directed evolution / designed protein
Function / homologyAnkyrin repeat-containing domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.26 Å
AuthorsHogan, B.J. / Fischer, G. / Houlihan, G. / Edmond, S. / Huovinen, T.T.K. / Hollfelder, F. / Hyvonen, M.
CitationJournal: To be published
Title: Designed Ankyrin Repeat Protein (DARPin) YTRL-2 selected by directed evolution against Lysozyme
Authors: Fischer, G.
History
DepositionAug 8, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 29, 2018Provider: repository / Type: Initial release
Revision 1.1May 8, 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: DARPin YTRL-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6113
Polymers18,1611
Non-polymers4502
Water1,40578
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area780 Å2
ΔGint-13 kcal/mol
Surface area7870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.487, 102.487, 96.714
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422
Components on special symmetry positions
IDModelComponents
11A-376-

HOH

21A-377-

HOH

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Components

#1: Protein DARPin YTRL-2


Mass: 18161.377 Da / Num. of mol.: 1 / Fragment: DARPin / Mutation: YTRL-2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Plasmid: pQE30 / Production host: Escherichia coli M15 (bacteria)
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-2PE / NONAETHYLENE GLYCOL


Mass: 414.488 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H38O10 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / Source method: isolated from a natural source / Formula: H2O

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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: 4.04 Å3/Da / Density % sol: 69.53 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7 / Details: 30% PEG3000, 0.1M Tris pH=7, 0.2M NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.259→65.393 Å / Num. obs: 14609 / % possible obs: 100 % / Redundancy: 52.3 % / Biso Wilson estimate: 66.59 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.014 / Rrim(I) all: 0.104 / Net I/σ(I): 33.4 / Num. measured all: 764056
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) all
2.259-2.26753.43.1460.6740.4313.176
10.472-65.39336.10.02410.0040.024

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Processing

Software
NameVersionClassification
Aimlessdata scaling
BUSTER2.10.3refinement
PDB_EXTRACT3.23data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.26→65.39 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.945 / SU R Cruickshank DPI: 0.166 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.176 / SU Rfree Blow DPI: 0.158 / SU Rfree Cruickshank DPI: 0.153
RfactorNum. reflection% reflectionSelection details
Rfree0.226 751 5.15 %RANDOM
Rwork0.196 ---
obs0.198 14591 100 %-
Displacement parametersBiso max: 144.34 Å2 / Biso mean: 66.45 Å2 / Biso min: 36.71 Å2
Baniso -1Baniso -2Baniso -3
1-4.6412 Å20 Å20 Å2
2--4.6412 Å20 Å2
3----9.2824 Å2
Refine analyzeLuzzati coordinate error obs: 0.29 Å
Refinement stepCycle: final / Resolution: 2.26→65.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1205 0 23 78 1306
Biso mean--103.27 70.86 -
Num. residues----161
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d451SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes40HARMONIC2
X-RAY DIFFRACTIONt_gen_planes181HARMONIC5
X-RAY DIFFRACTIONt_it1253HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion159SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1449SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1253HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg1693HARMONIC21.08
X-RAY DIFFRACTIONt_omega_torsion2.64
X-RAY DIFFRACTIONt_other_torsion19.18
LS refinement shellResolution: 2.26→2.44 Å / Rfactor Rfree error: 0 / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.2476 169 5.74 %
Rwork0.2202 2773 -
all0.2218 2942 -
obs--100 %

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