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Yorodumi- PDB-3dj8: Synthesis of (2S)-2-amino-7,8-epoxyoctanoic acid and structure of... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3dj8 | ||||||
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Title | Synthesis of (2S)-2-amino-7,8-epoxyoctanoic acid and structure of its metal-bridging complex with human arginase I | ||||||
Components | Arginase-1 | ||||||
Keywords | HYDROLASE / Epoxide binding / manganese cluster / Arginine metabolism / Disease mutation / Manganese / Metal-binding / Phosphoprotein / Urea cycle | ||||||
Function / homology | Function and homology information positive regulation of neutrophil mediated killing of fungus / Urea cycle / negative regulation of T-helper 2 cell cytokine production / arginase / arginase activity / arginine catabolic process to ornithine / urea cycle / negative regulation of type II interferon-mediated signaling pathway / defense response to protozoan / negative regulation of activated T cell proliferation ...positive regulation of neutrophil mediated killing of fungus / Urea cycle / negative regulation of T-helper 2 cell cytokine production / arginase / arginase activity / arginine catabolic process to ornithine / urea cycle / negative regulation of type II interferon-mediated signaling pathway / defense response to protozoan / negative regulation of activated T cell proliferation / arginine catabolic process / negative regulation of T cell proliferation / specific granule lumen / azurophil granule lumen / manganese ion binding / adaptive immune response / innate immune response / Neutrophil degranulation / extracellular space / extracellular region / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.51 Å | ||||||
Authors | Di Costanzo, L. / Christianson, D.W. | ||||||
Citation | Journal: Org.Biomol.Chem. / Year: 2008 Title: Synthesis of (2S)-2-amino-7,8-epoxyoctanoic acid and structure of its metal-bridging complex with human arginase I Authors: Zakharian, T.Y. / Di Costanzo, L. / Christianson, D.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3dj8.cif.gz | 136.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3dj8.ent.gz | 106.5 KB | Display | PDB format |
PDBx/mmJSON format | 3dj8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3dj8_validation.pdf.gz | 453.9 KB | Display | wwPDB validaton report |
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Full document | 3dj8_full_validation.pdf.gz | 468.5 KB | Display | |
Data in XML | 3dj8_validation.xml.gz | 28.7 KB | Display | |
Data in CIF | 3dj8_validation.cif.gz | 40.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dj/3dj8 ftp://data.pdbj.org/pub/pdb/validation_reports/dj/3dj8 | HTTPS FTP |
-Related structure data
Related structure data | 2zavS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 34779.879 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET11-D / Production host: Escherichia coli (E. coli) / References: UniProt: P05089, arginase #2: Chemical | ChemComp-MN / #3: Chemical | #4: 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: 2.37 Å3/Da / Density % sol: 48.12 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 25% JEFFAMINE, 100mM Hepes, 2.0mM Thymine. Soaking 40mM epoxide no thymine, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.51→50 Å / Num. obs: 99149 / % possible obs: 98.8 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Biso Wilson estimate: 21.8 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 3.6 |
Reflection shell | Resolution: 1.51→1.56 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.485 / Mean I/σ(I) obs: 3.6 / Num. unique all: 9976 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2ZAV Resolution: 1.51→50 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber Details: the data diffraction is affect by perfect twinning, twin fraction: 0.5; operator: -h, -k, l, the structure factor file is the untwinned structure factors that the depositor used for the refinement process.
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Refinement step | Cycle: LAST / Resolution: 1.51→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.51→1.56 Å
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