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- PDB-4mxr: Crystal structure of Trypanosoma cruzi formiminoglutamase with Mn2+2 -
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Open data
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Basic information
Entry | Database: PDB / ID: 4mxr | ||||||
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Title | Crystal structure of Trypanosoma cruzi formiminoglutamase with Mn2+2 | ||||||
![]() | Formiminoglutamase | ||||||
![]() | HYDROLASE / Arginase/deacetylase (a/b) fold | ||||||
Function / homology | ![]() putrescine biosynthetic process from arginine, using agmatinase / agmatinase activity / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Hai, Y. / Dugery, R.-J. / Healy, D. / Christianson, D.W. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 132.4 KB | Display | ![]() |
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PDB format | ![]() | 101.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 448.5 KB | Display | ![]() |
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Full document | ![]() | 451.3 KB | Display | |
Data in XML | ![]() | 24.7 KB | Display | |
Data in CIF | ![]() | 35 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4myfC ![]() 4mykC ![]() 4mylC ![]() 4mynC ![]() 2a0mS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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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.: 2 / Mutation: S302P Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-MN / #3: Chemical | ChemComp-GOL / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.97 Å3/Da / Density % sol: 37.6 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 4.9 Details: A 4 UL drop of protein solution [10 mg/mL protein, 50 mM bicine (pH 8.5), 100 UM MnCl2, 1 mM TCEP] was mixed with a 4 UL drop of precipitant solution [31% PEG 300, 0.1 M sodium acetate (pH 4. ...Details: A 4 UL drop of protein solution [10 mg/mL protein, 50 mM bicine (pH 8.5), 100 UM MnCl2, 1 mM TCEP] was mixed with a 4 UL drop of precipitant solution [31% PEG 300, 0.1 M sodium acetate (pH 4.9)] on a siliconized cover slide and equilibrated against a 500 UL reservoir of precipitant solution at 294K. The yielded crystal is apo. To obtain the Mn2+2 bound form, this apo-crystal was soaked with 5 mM MnCl2 in 0.1 M sodium malonate (pH 8.0), 27% PEG 3350) for 24 hours, VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 17, 2013 / 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: 1.85→50 Å / Num. obs: 44906 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.5 % / Rmerge(I) obs: 0.059 / Rsym value: 0.059 / Net I/σ(I): 14.162 |
Reflection shell | Resolution: 1.85→1.92 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.438 / Mean I/σ(I) obs: 2.013 / Rsym value: 0.438 / % possible all: 98.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2A0M Resolution: 1.849→21.964 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 0.06 / Phase error: 27 / 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: 40.001 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.849→21.964 Å
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Refine LS restraints |
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LS refinement shell |
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