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Yorodumi- PDB-6icc: The NZ-1 Fab complexed with the PDZ tandem fragment of A. aeolicu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6icc | ||||||||||||
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Title | The NZ-1 Fab complexed with the PDZ tandem fragment of A. aeolicus S2P homolog with the PA12 tag inserted between the residues 181 and 186 | ||||||||||||
Components |
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Keywords | SIGNALING PROTEIN / protease | ||||||||||||
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 | Aquifex aeolicus VF5 (bacteria) Rattus norvegicus (Norway rat) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||||||||
Authors | Tamura, R. / Oi, R. / Kaneko, M.K. / Kato, Y. / Nogi, T. | ||||||||||||
Funding support | Japan, 3items
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Citation | Journal: Protein Sci. / Year: 2019 Title: Application of the NZ-1 Fab as a crystallization chaperone for PA tag-inserted target proteins. Authors: Tamura, R. / Oi, R. / Akashi, S. / 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 | 6icc.cif.gz | 141.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6icc.ent.gz | 106.4 KB | Display | PDB format |
PDBx/mmJSON format | 6icc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6icc_validation.pdf.gz | 444.3 KB | Display | wwPDB validaton report |
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Full document | 6icc_full_validation.pdf.gz | 447.6 KB | Display | |
Data in XML | 6icc_validation.xml.gz | 25.4 KB | Display | |
Data in CIF | 6icc_validation.cif.gz | 36.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ic/6icc ftp://data.pdbj.org/pub/pdb/validation_reports/ic/6icc | HTTPS FTP |
-Related structure data
Related structure data | 6akqC 6al0C 6al1C 6icfC 3wklS 4yo0S 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 20721.291 Da / Num. of mol.: 1 / Fragment: UNP residues 115-181 and 185-292 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 |
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#2: Antibody | Mass: 23409.316 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Production host: Mus musculus (house mouse) |
#3: Antibody | Mass: 23347.764 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Production host: Mus musculus (house mouse) |
#4: Water | ChemComp-HOH / |
Sequence details | Authors state that four residues of the host protein, that is 182, 183, 184 and 185 were deleted ...Authors state that four residues of the host protein, that is 182, 183, 184 and 185 were deleted and 12 residues, GVAMPGAEDD |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.91 Å3/Da / Density % sol: 57.75 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 12-15%(wt./vol.) PEG 3350, 200mM sodium citrate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 24, 2018 |
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→48.23 Å / Num. obs: 54069 / % possible obs: 100 % / Redundancy: 6.7 % / CC1/2: 0.94 / Rmerge(I) obs: 0.056 / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 2→2.05 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.874 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 3874 / CC1/2: 0.873 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3wkl, 4yo0 Resolution: 2→48.23 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.936 / SU B: 5.299 / SU ML: 0.141 / Cross valid method: THROUGHOUT / ESU R: 0.174 / ESU R Free: 0.166
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.625 Å2
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Refinement step | Cycle: 1 / Resolution: 2→48.23 Å
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Refine LS restraints |
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