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Yorodumi- PDB-1hq5: CRYSTAL STRUCTURE OF THE BINUCLEAR MANGANESE METALLOENZYME ARGINA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1hq5 | ||||||
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Title | CRYSTAL STRUCTURE OF THE BINUCLEAR MANGANESE METALLOENZYME ARGINASE COMPLEXED WITH S-(2-BORONOETHYL)-L-CYSTEINE, AN L-ARGININE ANALOGUE | ||||||
Components | ARGINASE 1 | ||||||
Keywords | HYDROLASE / BINUCLEAR MANGANESE CLUSTER / BORONIC ACID INHIBITOR / PERFECTLY TWINNED CRYSTAL | ||||||
Function / homology | Function and homology information regulation of L-arginine import across plasma membrane / Urea cycle / collagen biosynthetic process / arginine metabolic process / mammary gland involution / positive regulation of neutrophil mediated killing of fungus / negative regulation of T-helper 2 cell cytokine production / arginase / response to selenium ion / arginase activity ...regulation of L-arginine import across plasma membrane / Urea cycle / collagen biosynthetic process / arginine metabolic process / mammary gland involution / positive regulation of neutrophil mediated killing of fungus / negative regulation of T-helper 2 cell cytokine production / arginase / response to selenium ion / arginase activity / arginine catabolic process to ornithine / negative regulation of type II interferon-mediated signaling pathway / urea cycle / response to methylmercury / response to vitamin A / response to herbicide / response to steroid hormone / response to manganese ion / Neutrophil degranulation / response to zinc ion / cellular response to glucagon stimulus / defense response to protozoan / response to amine / negative regulation of activated T cell proliferation / response to axon injury / response to vitamin E / response to amino acid / maternal process involved in female pregnancy / cellular response to interleukin-4 / cellular response to dexamethasone stimulus / response to cadmium ion / negative regulation of T cell proliferation / cellular response to transforming growth factor beta stimulus / positive regulation of endothelial cell proliferation / lung development / liver development / female pregnancy / response to peptide hormone / cellular response to hydrogen peroxide / manganese ion binding / cellular response to lipopolysaccharide / adaptive immune response / mitochondrial outer membrane / response to lipopolysaccharide / response to xenobiotic stimulus / innate immune response / neuronal cell body / extracellular space / identical protein binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.3 Å | ||||||
Authors | Kim, N.N. / Cox, J.D. / Baggio, R.F. / Emig, F.A. / Mistry, S.K. / Harper, S.L. / Speicher, D.W. / Morris Jr., S.M. / Ash, D.E. / Traish, A. / Christianson, D.W. | ||||||
Citation | Journal: Biochemistry / Year: 2001 Title: Probing erectile function: S-(2-boronoethyl)-L-cysteine binds to arginase as a transition state analogue and enhances smooth muscle relaxation in human penile corpus cavernosum. Authors: Kim, N.N. / Cox, J.D. / Baggio, R.F. / Emig, F.A. / Mistry, S.K. / Harper, S.L. / Speicher, D.W. / Morris Jr., S.M. / Ash, D.E. / Traish, A. / 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 | 1hq5.cif.gz | 127.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1hq5.ent.gz | 99.7 KB | Display | PDB format |
PDBx/mmJSON format | 1hq5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1hq5_validation.pdf.gz | 391.8 KB | Display | wwPDB validaton report |
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Full document | 1hq5_full_validation.pdf.gz | 402.9 KB | Display | |
Data in XML | 1hq5_validation.xml.gz | 14.9 KB | Display | |
Data in CIF | 1hq5_validation.cif.gz | 21.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hq/1hq5 ftp://data.pdbj.org/pub/pdb/validation_reports/hq/1hq5 | HTTPS FTP |
-Related structure data
Related structure data | |
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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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Details | the biological assembly is a trimer |
-Components
#1: Protein | Mass: 35019.098 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Production host: Escherichia coli (E. coli) / References: UniProt: P07824, 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: 2.38 Å3/Da / Density % sol: 48.38 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: PEG 1500, BICINE, manganese chloride, 2-(boronoethyl)-L-cysteine, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃Details: drop consists of equal amounts of protein and precipitant solutions | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Oct 13, 1999 / Details: mirrors |
Radiation | Monochromator: YALE MIRRORS / 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→20 Å / Num. all: 41944 / Num. obs: 41944 / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.9 % / Biso Wilson estimate: 31.1 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 8 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 2.85 % / Rmerge(I) obs: 0.242 / % possible all: 97.5 |
Reflection | *PLUS Num. obs: 14462 / % possible obs: 98.1 % / Num. measured all: 41944 |
Reflection shell | *PLUS % possible obs: 97.5 % |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 2.3→20 Å / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.3→20 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Num. reflection all: 14033 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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