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Yorodumi- PDB-8ipc: The recombinant NZ-1 Fab complexed with the PDZ tandem fragment o... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8ipc | ||||||
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Title | The recombinant NZ-1 Fab complexed with the PDZ tandem fragment of A. aeolicus S2P homolog with the PA14 tag inserted between the residues 181 and 184 | ||||||
Components |
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Keywords | IMMUNE SYSTEM/HYDROLASE / PDZ domain Fab / HYDROLASE / IMMUNE SYSTEM-HYDROLASE complex | ||||||
Function / homology | Function and homology information Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / metalloendopeptidase activity / proteolysis / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) Aquifex aeolicus VF5 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Adachi, Y. / Nogi, T. | ||||||
Funding support | Japan, 1items
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Citation | Journal: Protein Expr.Purif. / Year: 2023 Title: Recombinant production of antibody antigen-binding fragments with an N-terminal human growth hormone tag in mammalian cells. Authors: Adachi, Y. / Kaneko, M.K. / Kato, Y. / Nogi, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ipc.cif.gz | 164.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ipc.ent.gz | 102.3 KB | Display | PDB format |
PDBx/mmJSON format | 8ipc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ipc_validation.pdf.gz | 455.6 KB | Display | wwPDB validaton report |
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Full document | 8ipc_full_validation.pdf.gz | 462.8 KB | Display | |
Data in XML | 8ipc_validation.xml.gz | 24 KB | Display | |
Data in CIF | 8ipc_validation.cif.gz | 33.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ip/8ipc ftp://data.pdbj.org/pub/pdb/validation_reports/ip/8ipc | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Antibody | Mass: 23553.449 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Cell line (production host): Expi293F / Production host: Homo sapiens (human) |
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#2: Antibody | Mass: 23347.764 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Cell line (production host): Expi293F / Production host: Homo sapiens (human) |
#3: Protein | Mass: 21135.703 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aquifex aeolicus VF5 (bacteria) / Strain: VF5 / Gene: aq_1964 / Production host: Escherichia coli (E. coli) References: UniProt: O67776, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.53 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 14% (wt/vol) polyethylene glycol 3350, 0.2 M lithium sulfate, 0.1 M Bis-Tris-HCl (pH 6.5) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 15, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→45.82 Å / Num. obs: 35390 / % possible obs: 100 % / Redundancy: 6.7 % / Biso Wilson estimate: 46.97 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.076 / Net I/σ(I): 16.7 |
Reflection shell | Resolution: 2.2→2.27 Å / Rmerge(I) obs: 1.205 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 3029 / CC1/2: 0.738 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→38.32 Å / SU ML: 0.3567 / Cross valid method: FREE R-VALUE / σ(F): 0.02 / Phase error: 33.7384 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 62.38 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→38.32 Å
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Refine LS restraints |
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LS refinement shell |
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