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Yorodumi- PDB-4myf: Crystal structure of Trypanosoma cruzi formiminoglutamase(oxidize... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4myf | ||||||
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Title | Crystal structure of Trypanosoma cruzi formiminoglutamase(oxidized) with Mn2+2 at pH 6.0 | ||||||
Components | Formiminoglutamase | ||||||
Keywords | HYDROLASE / Arginase/deacetylase (a/b) fold | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Trypanosoma cruzi (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / 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 | 4myf.cif.gz | 74.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4myf.ent.gz | 53.2 KB | Display | PDB format |
PDBx/mmJSON format | 4myf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4myf_validation.pdf.gz | 424.9 KB | Display | wwPDB validaton report |
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Full document | 4myf_full_validation.pdf.gz | 426.4 KB | Display | |
Data in XML | 4myf_validation.xml.gz | 13.9 KB | Display | |
Data in CIF | 4myf_validation.cif.gz | 19.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/my/4myf ftp://data.pdbj.org/pub/pdb/validation_reports/my/4myf | HTTPS FTP |
-Related structure data
Related structure data | 4mxrC 4mykC 4mylC 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 / 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: 1.99 Å3/Da / Density % sol: 38.17 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6 Details: An apo-T.cruzi fromiminoglutamase(ox) crystal was soaked in 20 mM MnCl2, 0.1 M sodium malonate (pH 6.0), 25% PEG 3350 for 12 hours, VAPOR DIFFUSION, SITTING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 17, 2012 / 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: 1.8→50 Å / Num. obs: 24348 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Rmerge(I) obs: 0.117 / Rsym value: 0.117 / Net I/σ(I): 9.978 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.466 / Mean I/σ(I) obs: 2.273 / Rsym value: 0.466 / % possible all: 97.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2A0M Resolution: 1.799→25.14 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 0.09 / Phase error: 20.47 / 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: 37.915 Å2 / ksol: 0.336 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.799→25.14 Å
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Refine LS restraints |
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LS refinement shell |
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