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Yorodumi- PDB-4myn: Crystal structure of Trypanosoma cruzi formiminoglutamase N114H v... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4myn | ||||||
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Title | Crystal structure of Trypanosoma cruzi formiminoglutamase N114H variant with Mn2+2 | ||||||
Components | Formiminoglutamase | ||||||
Keywords | HYDROLASE / arginase/deacetylase (a/b) fold | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Trypanosoma cruzi (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.799 Å | ||||||
Authors | Hai, Y. / Dugery, R.J. / Healy, D. / Christianson, D.W. | ||||||
Citation | Journal: Biochemistry / Year: 2013 Title: Formiminoglutamase from trypanosoma cruzi is an arginase-like manganese metalloenzyme. Authors: Hai, Y. / Dugery, R.J. / Healy, D. / 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 | 4myn.cif.gz | 73.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4myn.ent.gz | 53 KB | Display | PDB format |
PDBx/mmJSON format | 4myn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/my/4myn ftp://data.pdbj.org/pub/pdb/validation_reports/my/4myn | HTTPS FTP |
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-Related structure data
Related structure data | 4mxrC 4myfC 4mykC 4mylC 2a0mS 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 34661.270 Da / Num. of mol.: 1 / Mutation: N114H, S302P Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Plasmid: pET vector / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q4DSA0, formimidoylglutamase | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.98 Å3/Da / Density % sol: 37.8 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: Apo-enzyme was crystallized in the following conditions: a 4 uL drop of protein solution [10 mg/mL protein, 50 mM bicine (pH 8.5), 100 uM MnCl2] was mixed with a 4 uL drop of precipitant ...Details: Apo-enzyme was crystallized in the following conditions: a 4 uL drop of protein solution [10 mg/mL protein, 50 mM bicine (pH 8.5), 100 uM MnCl2] was mixed with a 4 uL drop of precipitant solution [25% PEG 3350, 0.1 M sodium acetate (pH 4.6)] on a siliconized cover slide and equilibrated against a 500 uL reservoir of precipitant solution. To obtain the Mn2+ bound form, apo-crystal was soaked in 10 mM MnCl2, 0.1 M sodium malonate (pH 7.5), 27% PEG 3350 for 24 hours, VAPOR DIFFUSION, SITTING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 19, 2012 |
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.075 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 24658 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.3 % / Rmerge(I) obs: 0.088 / Rsym value: 0.088 / Net I/σ(I): 18.949 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.754 / Mean I/σ(I) obs: 2.966 / Rsym value: 0.754 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2A0M Resolution: 1.799→30.012 Å / SU ML: 0.21 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0.18 / Phase error: 23.67 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.837 Å2 / ksol: 0.348 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.1 Å2
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Refinement step | Cycle: LAST / Resolution: 1.799→30.012 Å
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Refine LS restraints |
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LS refinement shell |
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