+Open data
-Basic information
Entry | Database: PDB / ID: 2eiv | ||||||
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Title | Crystal Structure of the arginase from Thermus thermophilus | ||||||
Components | Arginase | ||||||
Keywords | HYDROLASE / Arginase / TTHA1496 / Thermus thermophilus / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information arginine metabolic process / arginase / arginase activity / metal ion binding Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.91 Å | ||||||
Authors | Kumarevel, T.S. / Karthe, P. / Kuramitsu, S. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2eiv.cif.gz | 590.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2eiv.ent.gz | 489.5 KB | Display | PDB format |
PDBx/mmJSON format | 2eiv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ei/2eiv ftp://data.pdbj.org/pub/pdb/validation_reports/ei/2eiv | HTTPS FTP |
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-Related structure data
Related structure data | 2ef4S S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 31270.146 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: TTHA1496 / Plasmid: pET-11a / Production host: Escherichia coli (E. coli) / References: UniProt: Q5SI78 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 51.08 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 8% PEG MME2000, 0.05M Bis Tris Propane pH7.0, 0.005M Ammonium Acetate, 0.1M Guanidine HCL, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 180 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å |
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Oct 9, 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: 2.9→40 Å / Num. all: 80781 / Num. obs: 80781 / % possible obs: 99.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Biso Wilson estimate: 37.7 Å2 / Rmerge(I) obs: 0.081 |
Reflection shell | Resolution: 2.9→3 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.449 / Num. unique all: 7915 / % possible all: 98.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2EF4 Resolution: 2.91→20 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2028337.98 / 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: 26.8685 Å2 / ksol: 0.309024 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 55.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.91→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→3.08 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
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Xplor file |
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