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- PDB-5oov: Designed Ankyrin Repeat Protein (DARPin) ETVD-1 in complex with L... -

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Basic information

Entry
Database: PDB / ID: 5oov
TitleDesigned Ankyrin Repeat Protein (DARPin) ETVD-1 in complex with Lysozyme
Components
  • DARPin ETVD-1
  • Lysozyme C
KeywordsDE NOVO PROTEIN / DARPin / directed evolution / designed protein / protein protein complex
Function / homology
Function and homology information


Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / defense response to bacterium ...Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / defense response to bacterium / endoplasmic reticulum / extracellular space / identical protein binding / cytoplasm
Similarity search - Function
Ankyrin repeat-containing domain / Lysozyme - #10 / Glycoside hydrolase, family 22, lysozyme / Glycoside hydrolase family 22 domain / Glycosyl hydrolases family 22 (GH22) domain signature. / Glycoside hydrolase, family 22 / C-type lysozyme/alpha-lactalbumin family / Glycosyl hydrolases family 22 (GH22) domain profile. / Alpha-lactalbumin / lysozyme C / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat ...Ankyrin repeat-containing domain / Lysozyme - #10 / Glycoside hydrolase, family 22, lysozyme / Glycoside hydrolase family 22 domain / Glycosyl hydrolases family 22 (GH22) domain signature. / Glycoside hydrolase, family 22 / C-type lysozyme/alpha-lactalbumin family / Glycosyl hydrolases family 22 (GH22) domain profile. / Alpha-lactalbumin / lysozyme C / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Lysozyme / Alpha Horseshoe / Lysozyme-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciessynthetic construct (others)
Gallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.365 Å
AuthorsHoulihan, G. / Fischer, G. / Hogan, B.J. / Edmond, S. / Huovinen, T.T.K. / Hollfelder, F. / Hyvonen, M.
CitationJournal: To be published
Title: Designed Ankyrin Repeat Protein (DARPin) ETVD-1 in complex with Lysozyme
Authors: Fischer, G.
History
DepositionAug 8, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 29, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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 ETVD-1
B: Lysozyme C


Theoretical massNumber of molelcules
Total (without water)32,4332
Polymers32,4332
Non-polymers00
Water5,332296
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1940 Å2
ΔGint-6 kcal/mol
Surface area12230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.913, 61.661, 53.344
Angle α, β, γ (deg.)90.000, 105.630, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-330-

HOH

21B-335-

HOH

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Components

#1: Protein DARPin ETVD-1


Mass: 18102.221 Da / Num. of mol.: 1 / Fragment: DARPin / Mutation: ETVD-1
Source method: isolated from a genetically manipulated source
Details: DARPin SNAP selection ETVD-1 / Source: (gene. exp.) synthetic construct (others) / Plasmid: pQE30 / Production host: Escherichia coli M15 (bacteria)
#2: Protein Lysozyme C / 1 / 4-beta-N-acetylmuramidase C / Allergen Gal d IV


Mass: 14331.160 Da / Num. of mol.: 1 / Fragment: Lysozyme / Source method: isolated from a natural source / Details: eggwhite / Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 296 / 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: 2.46 Å3/Da / Density % sol: 50.08 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 8 / Details: 0.2M Na-Tartrate, 14.7% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96864 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 8, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96864 Å / Relative weight: 1
ReflectionResolution: 1.365→52.065 Å / Num. obs: 66462 / % possible obs: 99.3 % / Redundancy: 17.2 % / Biso Wilson estimate: 22.56 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.012 / Rrim(I) all: 0.053 / Net I/σ(I): 26.8 / Num. measured all: 1140622
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
1.365-1.38911.41.2473647031970.8190.3851.3061.795.7
3.705-52.06517.80.046114234330.9990.010.04170.499.9

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Processing

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

5oos


Resolution: 1.365→52.065 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 23.45
RfactorNum. reflection% reflection
Rfree0.1794 3287 4.96 %
Rwork0.1485 --
obs0.1499 66322 99.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 83.42 Å2 / Biso mean: 38.1957 Å2 / Biso min: 19.17 Å2
Refinement stepCycle: final / Resolution: 1.365→52.065 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2160 0 0 296 2456
Biso mean---42.52 -
Num. residues----286
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072241
X-RAY DIFFRACTIONf_angle_d0.8493046
X-RAY DIFFRACTIONf_chiral_restr0.066340
X-RAY DIFFRACTIONf_plane_restr0.005402
X-RAY DIFFRACTIONf_dihedral_angle_d16.974815
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.3651-1.38550.33281360.35642612274895
1.3855-1.40710.31271470.32922664281196
1.4071-1.43020.33771500.29842625277596
1.4302-1.45490.32571370.27582663280097
1.4549-1.48130.31341410.24842694283597
1.4813-1.50980.28511210.212827362857100
1.5098-1.54060.24671450.188427492894100
1.5406-1.57410.18261430.163427732916100
1.5741-1.61080.18781610.15127042865100
1.6108-1.6510.15251480.136127352883100
1.651-1.69570.18551460.134227812927100
1.6957-1.74560.17281380.133127482886100
1.7456-1.80190.17961480.13427642912100
1.8019-1.86630.20941390.136727352874100
1.8663-1.94110.19951520.146827762928100
1.9411-2.02940.21591370.146327572894100
2.0294-2.13640.17611510.13727592910100
2.1364-2.27030.17771360.131427742910100
2.2703-2.44550.18831480.139827682916100
2.4455-2.69160.15891340.140427972931100
2.6916-3.08110.18261360.155227762912100
3.0811-3.88170.1811590.144327892948100
3.8817-52.10270.13571340.139128562990100

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