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- PDB-5oou: Designed Ankyrin Repeat Protein (DARPin) YTRL-1 selected by direc... -

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Basic information

Entry
Database: PDB / ID: 5oou
TitleDesigned Ankyrin Repeat Protein (DARPin) YTRL-1 selected by directed evolution against Lysozyme
ComponentsDARPin YTRL-1
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: 2.104 Å
AuthorsFischer, G. / Hogan, B.J. / Houlihan, G. / Edmond, S. / Huovinen, T.T.K. / Hollfelder, F. / Hyvonen, M.
CitationJournal: To be published
Title: Designed Ankyrin Repeat Protein (DARPin) YTRL-1 selected by directed evolution against Lysozyme
Authors: Fischer, G. / Hyvonen, M.
History
DepositionAug 8, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 29, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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-1


Theoretical massNumber of molelcules
Total (without water)18,1081
Polymers18,1081
Non-polymers00
Water1,802100
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.500, 103.500, 96.130
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422

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Components

#1: Protein DARPin YTRL-1


Mass: 18108.312 Da / Num. of mol.: 1 / Fragment: DARPin / Mutation: YTRL-1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Plasmid: pQE30 / Production host: Escherichia coli M15 (bacteria)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 4.1 Å3/Da / Density % sol: 69.96 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 8.5 / Details: 1.5M AmSO4, 0.1M Tris pH=8.5, 12% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.104→65.557 Å / Num. obs: 18216 / % possible obs: 100 % / Redundancy: 18.9 % / Biso Wilson estimate: 52.04 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.024 / Rrim(I) all: 0.103 / Net I/σ(I): 16.5 / Num. measured all: 343934
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.104-2.14202.485178948940.4750.5692.5511.498.9
5.71-65.55715.70.0541638510420.9990.0140.05640.5100

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
Aimlessdata scaling
PDB_EXTRACT3.23data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5OOS

5oos


Resolution: 2.104→44.817 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2063 908 4.99 %
Rwork0.1853 17275 -
obs0.1864 18183 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 163.71 Å2 / Biso mean: 63.404 Å2 / Biso min: 37.3 Å2
Refinement stepCycle: final / Resolution: 2.104→44.817 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1239 0 0 100 1339
Biso mean---69.49 -
Num. residues----165
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021265
X-RAY DIFFRACTIONf_angle_d0.4841720
X-RAY DIFFRACTIONf_chiral_restr0.035201
X-RAY DIFFRACTIONf_plane_restr0.003228
X-RAY DIFFRACTIONf_dihedral_angle_d16.572745
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.1041-2.23590.29991550.284228022957
2.2359-2.40860.30921310.247228282959
2.4086-2.65090.26361710.229928162987
2.6509-3.03450.24111400.208628673007
3.0345-3.82280.19391480.200229023050
3.8228-44.8270.18011630.15330603223

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