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Yorodumi- PDB-2pho: Crystal structure of human arginase I complexed with thiosemicarb... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2pho | ||||||
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Title | Crystal structure of human arginase I complexed with thiosemicarbazide at 1.95 resolution | ||||||
Components | Arginase-1 | ||||||
Keywords | HYDROLASE / THIOSEMICARBAZIDE / FRAGMENT / INHIBITOR DESIGN | ||||||
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 / negative regulation of type II interferon-mediated signaling pathway / urea cycle / 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 / negative regulation of type II interferon-mediated signaling pathway / urea cycle / 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 / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Di Costanzo, L. / Christianson, D.W. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2007 Title: Crystal structure of human arginase I complexed with thiosemicarbazide reveals an unusual thiocarbonyl mu-sulfide ligand in the binuclear manganese cluster. Authors: Di Costanzo, L. / Pique, M.E. / 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 | 2pho.cif.gz | 135.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2pho.ent.gz | 104.7 KB | Display | PDB format |
PDBx/mmJSON format | 2pho.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2pho_validation.pdf.gz | 450.5 KB | Display | wwPDB validaton report |
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Full document | 2pho_full_validation.pdf.gz | 472 KB | Display | |
Data in XML | 2pho_validation.xml.gz | 28.6 KB | Display | |
Data in CIF | 2pho_validation.cif.gz | 40.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ph/2pho ftp://data.pdbj.org/pub/pdb/validation_reports/ph/2pho | HTTPS FTP |
-Related structure data
Related structure data | 2phaC 2zavC 2aebS C: citing same article (ref.) 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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3 |
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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) / Gene: ARG1 / Plasmid: pBS(KS) / Production host: Escherichia coli (E. coli) / References: UniProt: P05089, arginase #2: Chemical | ChemComp-MN / #3: Chemical | ChemComp-TSZ / | #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: 294 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 12-22% Jeffamine ED-2001, 0.1 M Hepes, pH 7.0, 1.4 mM thiosemicarbazide, VAPOR DIFFUSION, HANGING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 19, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→40 Å / Num. obs: 42929 / % possible obs: 92 % / Observed criterion σ(I): 2 / Redundancy: 1.6 % / Biso Wilson estimate: 28.5 Å2 / Rmerge(I) obs: 0.146 / Net I/σ(I): 6.1 |
Reflection shell | Resolution: 1.95→2.05 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.322 / Mean I/σ(I) obs: 2.6 / Num. unique all: 4507 / % possible all: 97.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2AEB Resolution: 1.95→34.18 Å Details: From 40.0 and 34.18 A there are only very few reflections and the scaling process doesn't record those in the output file of structure factors because those have a poor profile. The data is ...Details: From 40.0 and 34.18 A there are only very few reflections and the scaling process doesn't record those in the output file of structure factors because those have a poor profile. The data is perfect hemihedral twinning with twinning operator: -h,-k,l and twinned fraction:0.5
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Refinement step | Cycle: LAST / Resolution: 1.95→34.18 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2.05 Å / Rfactor Rfree: 0.286 / Rfactor Rwork: 0.283 |