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Yorodumi- PDB-6al1: The NZ-1 Fab complexed with the PDZ tandem fragment of A. aeolicu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6al1 | ||||||||||||
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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 184 | ||||||||||||
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: 3.2 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 | 6al1.cif.gz | 115.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6al1.ent.gz | 85.6 KB | Display | PDB format |
PDBx/mmJSON format | 6al1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6al1_validation.pdf.gz | 455.4 KB | Display | wwPDB validaton report |
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Full document | 6al1_full_validation.pdf.gz | 457.7 KB | Display | |
Data in XML | 6al1_validation.xml.gz | 19.3 KB | Display | |
Data in CIF | 6al1_validation.cif.gz | 25.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/al/6al1 ftp://data.pdbj.org/pub/pdb/validation_reports/al/6al1 | HTTPS FTP |
-Related structure data
Related structure data | 6akqC 6al0C 6iccC 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: 20949.535 Da / Num. of mol.: 1 / Fragment: UNP residues 115-181 and 184-292 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) |
Sequence details | Authors state that two residues of the host protein, that is 182 and 183, were deleted and 12 ...Authors state that two residues of the host protein, that is 182 and 183, 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: 3.63 Å3/Da / Density % sol: 66.11 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 12%(wt./vol.) PEG 3350, 0.005M CoCl2, 5mM NiCl2, 5mM CdCl2, 5mM MgCl2, 100mM HEPES-Na (pH 7.5) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Nov 27, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→48.4 Å / Num. obs: 16978 / % possible obs: 100 % / Redundancy: 6.6 % / CC1/2: 0.932 / Rmerge(I) obs: 0.124 / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 3.2→3.42 Å / Redundancy: 6.8 % / Rmerge(I) obs: 1.17 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 3004 / CC1/2: 0.916 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3wkl, 4yo0 Resolution: 3.2→48.35 Å / Cor.coef. Fo:Fc: 0.904 / Cor.coef. Fo:Fc free: 0.889 / SU B: 35.736 / SU ML: 0.531 / Cross valid method: THROUGHOUT / ESU R: 2.878 / ESU R Free: 0.503 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 115.168 Å2
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Refinement step | Cycle: 1 / Resolution: 3.2→48.35 Å
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Refine LS restraints |
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