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- PDB-5op1: Designed Ankyrin Repeat Protein (DARPin) A4 in complex with Lysozyme -

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Basic information

Entry
Database: PDB / ID: 5op1
TitleDesigned Ankyrin Repeat Protein (DARPin) A4 in complex with Lysozyme
Components
  • DARPin A4
  • Lysozyme C
KeywordsDE NOVO PROTEIN / DARPin / directed evolution / designed protein / protein protein complex
Function / homology
Function and homology information


Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium ...Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / 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: 2.284 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) A4 in complex with Lysozyme
Authors: Fischer, G. / Hyvonen, M.
History
DepositionAug 9, 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 A4
B: Lysozyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2753
Polymers32,2392
Non-polymers351
Water1,45981
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, complex
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1840 Å2
ΔGint-11 kcal/mol
Surface area12620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.916, 102.866, 50.277
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein DARPin A4


Mass: 17908.029 Da / Num. of mol.: 1 / Fragment: DARPin / Mutation: A4
Source method: isolated from a genetically manipulated source
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: egg white / Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / 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: 2.24 Å3/Da / Density % sol: 45.15 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 8 / Details: 0.2 M (NH4)2 Tart, 20 %w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96858 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96858 Å / Relative weight: 1
ReflectionResolution: 2.284→55.916 Å / Num. obs: 13626 / % possible obs: 99.3 % / Redundancy: 12.8 % / Biso Wilson estimate: 41.41 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.024 / Rrim(I) all: 0.085 / Net I/σ(I): 21.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) all% possible all
2.284-2.32313.30.7760.9240.220.807100
6.196-55.91610.90.0380.9990.0130.0499.9

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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: 3OOS

3oos


Resolution: 2.284→51.433 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.19
RfactorNum. reflection% reflection
Rfree0.2495 683 5.02 %
Rwork0.2075 --
obs0.2098 13618 99.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 85.55 Å2 / Biso mean: 45.0915 Å2 / Biso min: 24.91 Å2
Refinement stepCycle: final / Resolution: 2.284→51.433 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2131 0 1 81 2213
Biso mean--52.06 42.28 -
Num. residues----282
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032166
X-RAY DIFFRACTIONf_angle_d0.5332936
X-RAY DIFFRACTIONf_chiral_restr0.037333
X-RAY DIFFRACTIONf_plane_restr0.003386
X-RAY DIFFRACTIONf_dihedral_angle_d13.4151295
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2837-2.460.35071320.265425342666100
2.46-2.70760.35691320.258325712703100
2.7076-3.09940.34491400.258425722712100
3.0994-3.90470.25891240.20922525264996
3.9047-51.4460.1851550.168527332888100

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