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Yorodumi- PDB-3p8p: Crystal Structure of Human Dimethylarginine Dimethylaminohydrolas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3p8p | ||||||
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Title | Crystal Structure of Human Dimethylarginine Dimethylaminohydrolase-1 (DDAH-1) variant C274S bound with N5-(1-iminopentyl)-L-ornithine | ||||||
Components | N(G),N(G)-dimethylarginine dimethylaminohydrolase 1 | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / DDAH / NITRIC OXIDE SYNTHASE REGULATOR / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | Function and homology information dimethylargininase / dimethylargininase activity / citrulline metabolic process / negative regulation of cellular response to hypoxia / arginine metabolic process / regulation of systemic arterial blood pressure / negative regulation of vascular permeability / amino acid binding / nitric oxide metabolic process / eNOS activation ...dimethylargininase / dimethylargininase activity / citrulline metabolic process / negative regulation of cellular response to hypoxia / arginine metabolic process / regulation of systemic arterial blood pressure / negative regulation of vascular permeability / amino acid binding / nitric oxide metabolic process / eNOS activation / nitric oxide mediated signal transduction / catalytic activity / arginine catabolic process / positive regulation of angiogenesis / positive regulation of nitric oxide biosynthetic process / negative regulation of cell population proliferation / extracellular exosome / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Monzingo, A.F. / Lluis, M. / Wang, Y. / Fast, W. / Robertus, J.D. | ||||||
Citation | Journal: Chemmedchem / Year: 2011 Title: Characterization of C-Alkyl Amidines as Bioavailable Covalent Reversible Inhibitors of Human DDAH-1. Authors: Lluis, M. / Wang, Y. / Monzingo, A.F. / Fast, W. / Robertus, J.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3p8p.cif.gz | 119.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3p8p.ent.gz | 90.6 KB | Display | PDB format |
PDBx/mmJSON format | 3p8p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p8/3p8p ftp://data.pdbj.org/pub/pdb/validation_reports/p8/3p8p | HTTPS FTP |
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-Related structure data
Related structure data | 3p8eC 3i2eS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 33607.430 Da / Num. of mol.: 2 / Mutation: C274S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DDAH, DDAH1 / Plasmid: PET28A-HDDAH-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O94760, dimethylargininase #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.06 Å3/Da / Density % sol: 40.27 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 23% polyethyleneglycol 6000, 0.1 M Tris-HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 26, 2010 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: double crystal, Si (111) liquid nitrogen cooled Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.5→20 Å / Num. obs: 18125 / % possible obs: 92 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.1 / Χ2: 2.332 / Net I/σ(I): 10.3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 3I2E Resolution: 2.5→20 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7282 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 32.9746 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 70.06 Å2 / Biso mean: 38.4638 Å2 / Biso min: 7.38 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→20 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16
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Xplor file |
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