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- PDB-7qnp: Designed Armadillo repeat protein N(A4)M4C(AII) co-crystallized w... -

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Basic information

Entry
Database: PDB / ID: 7qnp
TitleDesigned Armadillo repeat protein N(A4)M4C(AII) co-crystallized with hen egg white lysozyme
Components
  • Designed Armadillo Repeat Protein N(A4)M4C(AII)
  • Lysozyme
KeywordsHYDROLASE / armadillo / protein engineering / repeat protein / capping repeat
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
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-like domain superfamily
Similarity search - Domain/homology
1,4-DIETHYLENE DIOXIDE / Lysozyme C
Similarity search - Component
Biological speciessynthetic construct (others)
Gallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.586 Å
AuthorsMichel, E. / Mittl, P.R.E. / Plueckthun, A.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Union (EU)European Union
CitationJournal: Biochemistry / Year: 2023
Title: Improved Repeat Protein Stability by Combined Consensus and Computational Protein Design.
Authors: Michel, E. / Cucuzza, S. / Mittl, P.R.E. / Zerbe, O. / Pluckthun, A.
History
DepositionDec 21, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 8, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 15, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 25, 2023Group: Database references / Derived calculations / Category: atom_type / citation / citation_author
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.3Feb 7, 2024Group: Data collection / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_database_status / pdbx_initial_refinement_model
Item: _pdbx_database_status.deposit_site / _pdbx_database_status.status_code_sf
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Designed Armadillo Repeat Protein N(A4)M4C(AII)
BBB: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,11510
Polymers39,5932
Non-polymers5238
Water5,495305
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2090 Å2
ΔGint26 kcal/mol
Surface area16660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.592, 62.655, 108.740
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Designed Armadillo Repeat Protein N(A4)M4C(AII)


Mass: 25261.428 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Protein Lysozyme


Mass: 14331.160 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Production host: unidentified (others) / References: UniProt: P00698, lysozyme
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-DIO / 1,4-DIETHYLENE DIOXIDE


Mass: 88.105 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H8O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 305 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.43 Å3/Da / Density % sol: 49.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 35% (v/v) dioxane, pH undefined

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 9, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.586→42 Å / Num. obs: 53083 / % possible obs: 99.96 % / Redundancy: 13.4 % / CC1/2: 1 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.016 / Rrim(I) all: 0.059 / Net I/σ(I): 22.36
Reflection shellResolution: 1.586→1.65 Å / Redundancy: 13.8 % / Mean I/σ(I) obs: 1.48 / Num. unique obs: 5191 / CC1/2: 0.702 / Rpim(I) all: 0.384 / % possible all: 99.98

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5aei

5aei


Resolution: 1.586→41.997 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.957 / SU B: 4.013 / SU ML: 0.067 / Cross valid method: FREE R-VALUE / ESU R: 0.089 / ESU R Free: 0.09
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2185 2654 5 %
Rwork0.1865 50429 -
all0.188 --
obs-53083 99.876 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 32.885 Å2
Baniso -1Baniso -2Baniso -3
1--0.39 Å2-0 Å2-0 Å2
2---0.34 Å20 Å2
3---0.731 Å2
Refinement stepCycle: LAST / Resolution: 1.586→41.997 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2778 0 34 305 3117
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0133014
X-RAY DIFFRACTIONr_bond_other_d0.0090.0162906
X-RAY DIFFRACTIONr_angle_refined_deg2.171.6184104
X-RAY DIFFRACTIONr_angle_other_deg1.7171.5766681
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7175397
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.18325148
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.51115512
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2611513
X-RAY DIFFRACTIONr_chiral_restr0.1230.2390
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.023582
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02688
X-RAY DIFFRACTIONr_nbd_refined0.2390.2762
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1930.22757
X-RAY DIFFRACTIONr_nbtor_refined0.1710.21475
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0880.21403
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2850.2201
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0780.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1990.223
X-RAY DIFFRACTIONr_nbd_other0.3180.288
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3230.228
X-RAY DIFFRACTIONr_mcbond_it2.2722.4441549
X-RAY DIFFRACTIONr_mcbond_other2.2552.4411548
X-RAY DIFFRACTIONr_mcangle_it3.0523.651959
X-RAY DIFFRACTIONr_mcangle_other3.0563.6531960
X-RAY DIFFRACTIONr_scbond_it3.4222.9751465
X-RAY DIFFRACTIONr_scbond_other3.422.9751466
X-RAY DIFFRACTIONr_scangle_it5.2734.2772145
X-RAY DIFFRACTIONr_scangle_other5.2724.2782146
X-RAY DIFFRACTIONr_lrange_it6.91431.5983659
X-RAY DIFFRACTIONr_lrange_other6.79430.9153584
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.586-1.6270.41910.42536310.42338740.7380.76298.65770.415
1.627-1.6720.3791890.36735810.36837700.8310.8391000.355
1.672-1.720.3421850.31635080.31736930.8620.881000.301
1.72-1.7730.3541780.28533820.28835620.8610.89999.94390.265
1.773-1.8310.2771730.23332810.23534550.9120.93199.97110.21
1.831-1.8950.2381670.20231860.20433540.920.93699.97020.177
1.895-1.9670.2221620.18130990.18332610.9360.9461000.161
1.967-2.0470.2041560.16829570.1731130.940.9571000.15
2.047-2.1370.2061500.17528410.17629910.9430.9551000.16
2.137-2.2410.2131440.17427440.17628880.9440.9561000.159
2.241-2.3620.2041370.1725970.17127340.9490.9591000.156
2.362-2.5050.2111310.16624780.16826130.9490.95799.84690.156
2.505-2.6770.2171220.16723140.16924370.9450.95599.9590.159
2.677-2.8910.1941140.15721620.15922760.9560.9651000.153
2.891-3.1650.191050.17120240.17221290.9560.9581000.169
3.165-3.5360.196960.18218420.18319380.9590.9581000.185
3.536-4.0790.188860.1616260.16217120.9660.971000.172
4.079-4.9840.175740.1613890.1614650.9690.97299.86350.182
4.984-6.9990.291590.24511170.24711760.9350.9431000.262
6.999-41.9970.261350.2026700.2057050.9410.9591000.248
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.20390.43220.22720.38610.40240.50570.15950.0618-0.07770.1242-0.0905-0.08020.0982-0.1598-0.0690.0875-0.0233-0.04080.08070.00720.03339.369736.152244.9981
20.21790.0676-0.30361.07350.01680.80120.0256-0.0378-0.02430.03030.00510.0194-0.03440.0691-0.03070.00820.00220.00820.01730.01650.050355.092660.565933.1885
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLAAA2 - 241
2X-RAY DIFFRACTION1ALLAaA301
3X-RAY DIFFRACTION1ALLAbA302
4X-RAY DIFFRACTION1ALLAcA303
5X-RAY DIFFRACTION1ALLAdA304
6X-RAY DIFFRACTION2ALLBBB1 - 129
7X-RAY DIFFRACTION2ALLBaB201
8X-RAY DIFFRACTION2ALLBbB202

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