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

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Basic information

Entry
Database: PDB / ID: 5ooy
TitleDesigned Ankyrin Repeat Protein (DARPin) VHAH-1 in complex with Lysozyme
Components
  • DARPin VHAH-1
  • 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 / Lysozyme ...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 / Lysozyme / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Lysozyme-like domain superfamily / Alpha Horseshoe / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciessynthetic construct (others)
Gallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 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) VHAH-1 in complex with Lysozyme
Authors: Hogan, B.J. / 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
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DARPin VHAH-1
B: Lysozyme C
E: DARPin VHAH-1
F: Lysozyme C


Theoretical massNumber of molelcules
Total (without water)64,9574
Polymers64,9574
Non-polymers00
Water7,170398
1
A: DARPin VHAH-1
B: Lysozyme C


Theoretical massNumber of molelcules
Total (without water)32,4792
Polymers32,4792
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1710 Å2
ΔGint-5 kcal/mol
Surface area12840 Å2
MethodPISA
2
E: DARPin VHAH-1
F: Lysozyme C


Theoretical massNumber of molelcules
Total (without water)32,4792
Polymers32,4792
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1780 Å2
ΔGint-5 kcal/mol
Surface area12400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.773, 81.052, 89.387
Angle α, β, γ (deg.)90.000, 94.010, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein DARPin VHAH-1


Mass: 18147.369 Da / Num. of mol.: 2 / Fragment: DARPin / Mutation: VHAH-1
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.: 2 / Fragment: Lysozyme / Source method: isolated from a natural source / Details: egg white / Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 398 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.09 Å3/Da / Density % sol: 41.28 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 8 / Details: 10% PEG3000, 0.1M Imidazole pH=8.0, 0.2M LiSO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97626 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97626 Å / Relative weight: 1
ReflectionResolution: 1.718→81.052 Å / Num. obs: 55206 / % possible obs: 98.9 % / Redundancy: 3.4 % / Biso Wilson estimate: 29.43 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.048 / Rrim(I) all: 0.089 / Net I/σ(I): 8.8 / Num. measured all: 185561
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
1.718-1.7473.40.969962428020.5560.6111.1481.398.6
4.662-81.0523.10.041871727790.9970.0270.0492197.4

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
Aimlessdata scaling
PDB_EXTRACT3.23data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5OOV

5oov


Resolution: 1.72→44.58 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.923 / SU R Cruickshank DPI: 0.121 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.124 / SU Rfree Blow DPI: 0.115 / SU Rfree Cruickshank DPI: 0.114
RfactorNum. reflection% reflectionSelection details
Rfree0.224 2760 5.02 %RANDOM
Rwork0.192 ---
obs0.194 54951 98.8 %-
Displacement parametersBiso max: 114.14 Å2 / Biso mean: 32.12 Å2 / Biso min: 15.92 Å2
Baniso -1Baniso -2Baniso -3
1--6.3563 Å20 Å2-4.805 Å2
2--0.4414 Å20 Å2
3---5.915 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: final / Resolution: 1.72→44.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4362 0 0 398 4760
Biso mean---41.15 -
Num. residues----575
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1555SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes123HARMONIC2
X-RAY DIFFRACTIONt_gen_planes673HARMONIC5
X-RAY DIFFRACTIONt_it4510HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion580SEMIHARMONIC5
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_contact5625SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d4510HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg6125HARMONIC21
X-RAY DIFFRACTIONt_omega_torsion3.04
X-RAY DIFFRACTIONt_other_torsion17.12
LS refinement shellResolution: 1.72→1.76 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.26 211 5.19 %
Rwork0.2335 3853 -
all0.2349 4064 -
obs--98.82 %

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