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- PDB-7pa5: Complex between the beta-lactamase CMY-2 with an inhibitory nanobody -
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Open data
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Basic information
Entry | Database: PDB / ID: 7pa5 | ||||||
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Title | Complex between the beta-lactamase CMY-2 with an inhibitory nanobody | ||||||
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![]() | HYDROLASE / Single Domain Camelid Antibody Cephalosporinase | ||||||
Function / homology | ![]() antibiotic catabolic process / beta-lactamase activity / beta-lactamase / outer membrane-bounded periplasmic space / response to antibiotic Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Frederic Cawez, F.C. / Frederic Kerff, F.K. / Moreno Galleni, M.G. / Raphael Herman, R.H. | ||||||
![]() | ![]() Title: Development of Nanobodies as Theranostic Agents against CMY-2-Like Class C beta-Lactamases. Authors: Cawez, F. / Mercuri, P.S. / Morales-Yanez, F.J. / Maalouf, R. / Vandevenne, M. / Kerff, F. / Guerin, V. / Mainil, J. / Thiry, D. / Saulmont, M. / Vanderplasschen, A. / Lafaye, P. / Ayme, G. ...Authors: Cawez, F. / Mercuri, P.S. / Morales-Yanez, F.J. / Maalouf, R. / Vandevenne, M. / Kerff, F. / Guerin, V. / Mainil, J. / Thiry, D. / Saulmont, M. / Vanderplasschen, A. / Lafaye, P. / Ayme, G. / Bogaerts, P. / Dumoulin, M. / Galleni, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 187.7 KB | Display | ![]() |
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PDB format | ![]() | 150.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 455.6 KB | Display | ![]() |
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Full document | ![]() | 460.9 KB | Display | |
Data in XML | ![]() | 18.4 KB | Display | |
Data in CIF | ![]() | 24.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1zc2S ![]() 6gkuS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 39896.492 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: bla CMY-2, ampC, blaCMY-2, blacmy-2, blaCMY-2-1, CMY-2, cmy-2, A9819_28690, AM333_27370, AM464_28260, APX88_19125, BB545_24720, BHS81_30845, BIQ87_27420, BIU72_25045, BK248_14575, BK292_11440, ...Gene: bla CMY-2, ampC, blaCMY-2, blacmy-2, blaCMY-2-1, CMY-2, cmy-2, A9819_28690, AM333_27370, AM464_28260, APX88_19125, BB545_24720, BHS81_30845, BIQ87_27420, BIU72_25045, BK248_14575, BK292_11440, BK375_28010, BWI89_23710, CWM24_03220, D2184_22885, D2185_19815, D2188_23590, D9D43_21375, D9D43_30790, DS732_29990, E2129_13225, EAN77_15185, ED648_23630, ED648_28285, EJC75_03830, EJC75_22930, ELT58_15290, EO241_21750, FKC84_16435, HMQ05_23325, HMQ05_27045, HND23_22080, HND23_27950, HVX28_23930, HVZ20_24300, HVZ21_14455, KPCE_053, pAPEC1990_61_74, pAR060302_0084, pAR060302_81, peH4H_0073, pESCR_00001, WR15_23065 Production host: ![]() ![]() |
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#2: Antibody | Mass: 14207.594 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#3: Chemical | ChemComp-GOL / |
#4: Chemical | ChemComp-PO4 / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.93 Å3/Da / Density % sol: 58.05 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: PEG400, glycerol, Ammonium tartarate, tris HCl, |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 2, 2021 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.18→48.885 Å / Num. obs: 11589 / % possible obs: 99.6 % / Redundancy: 37.789 % / Biso Wilson estimate: 76.74 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.709 / Rrim(I) all: 0.719 / Χ2: 0.599 / Net I/σ(I): 7.09 / Num. measured all: 437933 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1ZC2 (CMY-2), 6GKU (nanobody) Resolution: 3.184→48.885 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 25.5 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 187.84 Å2 / Biso mean: 78.8152 Å2 / Biso min: 38.08 Å2 | ||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.184→48.885 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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