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Open data
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Basic information
Entry | Database: PDB / ID: 2ef4 | ||||||
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Title | Crystal structure of the arginase from thermus thermophilus | ||||||
![]() | Arginase | ||||||
![]() | HYDROLASE / Arginase / ttha1496 / thermus thermophilus / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | ![]() arginase / arginase activity / arginine catabolic process to ornithine / manganese ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kumarevel, T.S. / Karthe, P. / Kuramitsu, S. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
![]() | ![]() Title: Crystal structure of the arginase from thermus thermophilus Authors: Kumarevel, T.S. / Karthe, P. / Kuramitsu, S. / Yokoyama, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 60.3 KB | Display | ![]() |
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PDB format | ![]() | 43.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 423.7 KB | Display | ![]() |
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Full document | ![]() | 428.3 KB | Display | |
Data in XML | ![]() | 12.1 KB | Display | |
Data in CIF | ![]() | 16.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2ef5C ![]() 5cevS C: citing same article ( S: Starting model for refinement |
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Similar structure data | |
Other databases |
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Links
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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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Details | multimer. may form hexamer using y+1/2,x+1/2,-z+1/2; -x+1/2, -z+1/2, -y+1/2; z+1/2, -y+1/2, x+1/2; x, y+1, z+1; -z,-x+1, y+1; -y, z+1, -x+1 |
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Components
#1: Protein | Mass: 31138.951 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.81 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 50% PEG 200, 0.1M Citrate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 180 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Oct 4, 2006 |
Radiation | Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. all: 14250 / Num. obs: 14250 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 40.5 % / Biso Wilson estimate: 30.8 Å2 / Rmerge(I) obs: 0.063 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 42.6 % / Rmerge(I) obs: 0.474 / Num. unique all: 1384 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5CEV Resolution: 2.3→19.99 Å / Rfactor Rfree error: 0.013 / Data cutoff high absF: 582402.5 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 48.3647 Å2 / ksol: 0.365564 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→19.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Total num. of bins used: 6 /
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Xplor file |
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