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Yorodumi- PDB-1zli: Crystal structure of the tick carboxypeptidase inhibitor in compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1zli | ||||||
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Title | Crystal structure of the tick carboxypeptidase inhibitor in complex with human carboxypeptidase B | ||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR / inhibitor-metallocarboxypeptidase complex / beta-defensin fold (TCI) / eight-stranded twisted beta-sheet surrounded by eight alpha-helices (CPB) / HYDROLASE-HYDROLASE INHIBITOR COMPLEX | ||||||
Function / homology | Function and homology information acquisition of nutrients from host / carboxypeptidase B / metalloendopeptidase inhibitor activity / enzyme inhibitor activity / Metabolism of Angiotensinogen to Angiotensins / metallocarboxypeptidase activity / carboxypeptidase activity / blood coagulation / toxin activity / cytoplasmic vesicle ...acquisition of nutrients from host / carboxypeptidase B / metalloendopeptidase inhibitor activity / enzyme inhibitor activity / Metabolism of Angiotensinogen to Angiotensins / metallocarboxypeptidase activity / carboxypeptidase activity / blood coagulation / toxin activity / cytoplasmic vesicle / proteolysis / extracellular space / zinc ion binding / extracellular region Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Rhipicephalus bursa (arthropod) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.09 Å | ||||||
Authors | Arolas, J.L. / Popowicz, G.M. / Lorenzo, J. / Sommerhoff, C.P. / Huber, R. / Aviles, F.X. / Holak, T.A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2005 Title: The Three-Dimensional Structures of Tick Carboxypeptidase Inhibitor in Complex with A/B Carboxypeptidases Reveal a Novel Double-headed Binding Mode Authors: Arolas, J.L. / Popowicz, G.M. / Lorenzo, J. / Sommerhoff, C.P. / Huber, R. / Aviles, F.X. / Holak, T.A. #1: Journal: J.Biol.Chem. / Year: 2005 Title: A carboxypeptidase inhibitor from the tick Rhipicephalus bursa: isolation, cDNA cloning, recombinant expression, and characterization Authors: Arolas, J.L. / Lorenzo, J. / Rovira, A. / Castella, J. / Aviles, F.X. / Sommerhoff, C.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1zli.cif.gz | 97.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1zli.ent.gz | 76.2 KB | Display | PDB format |
PDBx/mmJSON format | 1zli.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1zli_validation.pdf.gz | 438 KB | Display | wwPDB validaton report |
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Full document | 1zli_full_validation.pdf.gz | 440.8 KB | Display | |
Data in XML | 1zli_validation.xml.gz | 21.2 KB | Display | |
Data in CIF | 1zli_validation.cif.gz | 32.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zl/1zli ftp://data.pdbj.org/pub/pdb/validation_reports/zl/1zli | HTTPS FTP |
-Related 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: 35127.465 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pPIC9 / Production host: Pichia pastoris (fungus) / Strain (production host): KM71 / References: UniProt: P15086, carboxypeptidase B |
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#2: Protein | Mass: 7945.104 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhipicephalus bursa (arthropod) / Plasmid: pBAT4 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: GenBank: 58374130, UniProt: Q5EPH2*PLUS |
#3: Chemical | ChemComp-ZN / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 53.7 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.1M bis-tris, 0.2M lithium sulfate monohydrate, 25%(w/v) PEG 3350, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 21, 2004 / Details: mirror |
Radiation | Monochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. all: 31725 / Num. obs: 27650 / % possible obs: 87 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
Reflection shell | Resolution: 2→2.1 Å / % possible all: 39.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.09→19.96 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.936 / SU B: 3.679 / SU ML: 0.099 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.176 / ESU R Free: 0.165 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.376 Å2
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Refinement step | Cycle: LAST / Resolution: 2.09→19.96 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.09→2.144 Å / Total num. of bins used: 20 /
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