+Open data
-Basic information
Entry | Database: PDB / ID: 1itq | ||||||
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Title | HUMAN RENAL DIPEPTIDASE | ||||||
Components | RENAL DIPEPTIDASEMembrane dipeptidase | ||||||
Keywords | HYDROLASE / DIPEPTIDASE / GLYCOPROTEIN / MEMBRANE-BOUND / ZINC PROTEASE BETA-LACTAMASE / CILASTATIN / COMPLEX (HYDROLASE-INHIBITOR) | ||||||
Function / homology | Function and homology information lactam catabolic process / leukotriene D4 catabolic process / membrane dipeptidase / GPI anchor binding / antibiotic metabolic process / LTC4-CYSLTR mediated IL4 production / glutathione catabolic process / modified amino acid binding / homocysteine metabolic process / Aflatoxin activation and detoxification ...lactam catabolic process / leukotriene D4 catabolic process / membrane dipeptidase / GPI anchor binding / antibiotic metabolic process / LTC4-CYSLTR mediated IL4 production / glutathione catabolic process / modified amino acid binding / homocysteine metabolic process / Aflatoxin activation and detoxification / metallodipeptidase activity / Synthesis of Leukotrienes (LT) and Eoxins (EX) / dipeptidase activity / metalloexopeptidase activity / microvillus membrane / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / cellular response to nitric oxide / glutathione metabolic process / side of membrane / cellular response to calcium ion / neutrophil chemotaxis / negative regulation of cell migration / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / beta-lactamase activity / beta-lactamase / cellular response to xenobiotic stimulus / apical part of cell / cell junction / inflammatory response / apical plasma membrane / negative regulation of apoptotic process / proteolysis / extracellular space / extracellular exosome / zinc ion binding / nucleoplasm / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MIR / Resolution: 2.3 Å | ||||||
Authors | Nitanai, Y. / Satow, Y. / Adachi, H. / Tsujimoto, M. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2002 Title: Crystal Structure of Human Renal Dipeptidase Involved in beta-Lactam Hydrolysis Authors: Nitanai, Y. / Satow, Y. / Adachi, H. / Tsujimoto, M. #1: Journal: J.CRYST.GROWTH / Year: 1996 Title: Crystallization and preliminary X-ray investigation of a glycoprotein, human renal dipeptidase Authors: Nitanai, Y. / Satow, Y. / Adachi, H. / Tsujimoto, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1itq.cif.gz | 157.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1itq.ent.gz | 125.2 KB | Display | PDB format |
PDBx/mmJSON format | 1itq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/it/1itq ftp://data.pdbj.org/pub/pdb/validation_reports/it/1itq | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological assembly is a dimer corresponding to the dimer in the asymmetric unit. |
-Components
#1: Protein | Mass: 41108.195 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Tissue: renal cortex / Plasmid: PHILD2 / Production host: Pichia pastoris (fungus) / Strain (production host): GS115 / References: UniProt: P16444, membrane dipeptidase #2: Sugar | ChemComp-NAG / #3: Chemical | ChemComp-ZN / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 10 |
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-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.7 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 283 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: PEG 8000, HEPES, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 283.0K | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 10 ℃ / Details: Nitanai, Y., (1996) J.CRYST.GROWTH, 168, 280. | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 277 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: May 22, 1996 / Details: MIRRORS |
Radiation | Monochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→30 Å / Num. all: 30657 / Num. obs: 30657 / % possible obs: 92.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 5.6 % / Biso Wilson estimate: 21.09 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 11 |
Reflection shell | Resolution: 2.3→2.35 Å / Rmerge(I) obs: 0.163 / % possible all: 79.5 |
Reflection | *PLUS Lowest resolution: 30 Å / Num. measured all: 174691 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 2.3→10 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2.3 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 21.79 Å2 | ||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.35 Å / Total num. of bins used: 15
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Xplor file |
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Refinement | *PLUS % reflection Rfree: 10 % | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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