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Yorodumi- PDB-4n1h: Structure of a single-domain camelid antibody fragment cAb-F11N i... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4n1h | ||||||
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Title | Structure of a single-domain camelid antibody fragment cAb-F11N in complex with the BlaP beta-lactamase from Bacillus licheniformis | ||||||
Components |
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Keywords | HYDROLASE/IMMUNE SYSTEM / Immunoglobulin fold / Antigen binding / HYDROLASE-IMMUNE SYSTEM complex | ||||||
Function / homology | Function and homology information beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic / plasma membrane Similarity search - Function | ||||||
Biological species | Bacillus licheniformis (bacteria) Lama glama (llama) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Pain, C. / Kerff, F. / Herman, R. / Sauvage, E. / Preumont, S. / Charlier, P. / Dumoulin, M. | ||||||
Citation | Journal: To be Published Title: Probing the mechanism of aggregation of polyQ model proteins with camelid heavy-chain antibody fragments Authors: Pain, C. / Cosolo, A. / Preumont, S. / Scarafone, N. / Thorn, D. / Herman, R. / Spiegel, H. / Pardon, E. / Matagne, A. / Charlier, P. / Steyaert, J. / Damblon, C. / Kerff, F. / Esposito, G. / Dumoulin, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4n1h.cif.gz | 157.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4n1h.ent.gz | 123.6 KB | Display | PDB format |
PDBx/mmJSON format | 4n1h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4n1h_validation.pdf.gz | 455.6 KB | Display | wwPDB validaton report |
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Full document | 4n1h_full_validation.pdf.gz | 473.5 KB | Display | |
Data in XML | 4n1h_validation.xml.gz | 28.9 KB | Display | |
Data in CIF | 4n1h_validation.cif.gz | 39.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n1/4n1h ftp://data.pdbj.org/pub/pdb/validation_reports/n1/4n1h | HTTPS FTP |
-Related structure data
Related structure data | 4m3jSC 4m3kC 5lwfC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 30412.311 Da / Num. of mol.: 2 / Fragment: UNP residues 44-307 / Mutation: ProGly insertion between residues 197 and 198 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus licheniformis (bacteria) / Gene: penP, blaP / Plasmid: pNY / Production host: Escherichia coli (E. coli) / References: UniProt: P00808, beta-lactamase #2: Antibody | Mass: 14609.050 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lama glama (llama) / Plasmid: pMES4 / Production host: Escherichia coli (E. coli) / Strain (production host): TG1 #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.68 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 0.1 uL acetate 0.1 M, pH 4.6, 12 % P4K + 0.1 uL protein complex at 14 mg/mL in Tris 20 mM, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98011 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 9, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98011 Å / Relative weight: 1 |
Reflection | Resolution: 3→75.44 Å / Num. all: 15849 / Num. obs: 15849 / % possible obs: 99.5 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.185 / Net I/σ(I): 5.4 |
Reflection shell | Resolution: 3→3.16 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.505 / Mean I/σ(I) obs: 2.4 / % possible all: 99.6 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4M3J Resolution: 3→75.44 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.858 / Cross valid method: THROUGHOUT / ESU R Free: 0.548 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.72 Å2
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Refinement step | Cycle: LAST / Resolution: 3→75.44 Å
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Refine LS restraints |
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