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Yorodumi- PDB-4myl: Crystal structure of Trypanosoma cruzi Formiminoglutamase (oxidiz... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4myl | ||||||
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Title | Crystal structure of Trypanosoma cruzi Formiminoglutamase (oxidized) at pH 4.6 | ||||||
Components | Formiminoglutamase | ||||||
Keywords | HYDROLASE / arginase/deacetylase (a/b) fold | ||||||
Function / homology | Function and homology information putrescine biosynthetic process from arginine, using agmatinase / agmatinase activity / metal ion binding Similarity search - Function | ||||||
Biological species | Trypanosoma cruzi (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.531 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 | 4myl.cif.gz | 72.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4myl.ent.gz | 52.6 KB | Display | PDB format |
PDBx/mmJSON format | 4myl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4myl_validation.pdf.gz | 421.1 KB | Display | wwPDB validaton report |
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Full document | 4myl_full_validation.pdf.gz | 422.6 KB | Display | |
Data in XML | 4myl_validation.xml.gz | 13.3 KB | Display | |
Data in CIF | 4myl_validation.cif.gz | 19 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/my/4myl ftp://data.pdbj.org/pub/pdb/validation_reports/my/4myl | HTTPS FTP |
-Related structure data
Related structure data | 4mxrC 4myfC 4mykC 4mynC 2a0mS 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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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 34637.227 Da / Num. of mol.: 1 / Mutation: 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: 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: 37.92 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 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 ...Details: 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, VAPOR DIFFUSION, HANGING 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: Jul 27, 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 twin | Operator: h,-h-k,-l / Fraction: 0.282 |
Reflection | Resolution: 1.53→50 Å / Num. obs: 40029 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Rmerge(I) obs: 0.077 / Rsym value: 0.077 / Net I/σ(I): 24.071 |
Reflection shell | Resolution: 1.53→1.58 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.534 / Mean I/σ(I) obs: 2.224 / Rsym value: 0.534 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2a0m Resolution: 1.531→37.365 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0.14 / Phase error: 22.86 / Stereochemistry target values: TWIN_LSQ_F
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.545 Å2 / ksol: 0.373 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.448 Å2
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Refinement step | Cycle: LAST / Resolution: 1.531→37.365 Å
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Refine LS restraints |
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LS refinement shell |
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