+Open data
-Basic information
Entry | Database: PDB / ID: 2cev | ||||||
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Title | ARGINASE FROM BACILLUS CALDEVELOX, NATIVE STRUCTURE AT PH 8.5 | ||||||
Components | PROTEIN (ARGINASE) | ||||||
Keywords | HYDROLASE / ENZYME / ARGININE HYDROLYSIS / NITROGEN METABOLISM / MANGANESE METALLOENZYME | ||||||
Function / homology | Function and homology information arginase / arginase activity / arginine catabolic process to ornithine / urea cycle / manganese ion binding / cytosol Similarity search - Function | ||||||
Biological species | Bacillus caldovelox (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | ||||||
Authors | Bewley, M.C. / Jeffrey, P.D. / Patchett, M.L. / Kanyo, Z.F. / Baker, E.N. | ||||||
Citation | Journal: Structure Fold.Des. / Year: 1999 Title: Crystal structures of Bacillus caldovelox arginase in complex with substrate and inhibitors reveal new insights into activation, inhibition and catalysis in the arginase superfamily. Authors: Bewley, M.C. / Jeffrey, P.D. / Patchett, M.L. / Kanyo, Z.F. / Baker, E.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2cev.cif.gz | 354.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2cev.ent.gz | 289.1 KB | Display | PDB format |
PDBx/mmJSON format | 2cev.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2cev_validation.pdf.gz | 412.6 KB | Display | wwPDB validaton report |
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Full document | 2cev_full_validation.pdf.gz | 427.3 KB | Display | |
Data in XML | 2cev_validation.xml.gz | 34.7 KB | Display | |
Data in CIF | 2cev_validation.cif.gz | 54.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ce/2cev ftp://data.pdbj.org/pub/pdb/validation_reports/ce/2cev | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 32476.248 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus caldovelox (bacteria) / Strain: BACILLUS SPECIES DSM 411 / Cell line (production host): BL21 / Production host: Escherichia coli (E. coli) / References: UniProt: P53608, arginase #2: Chemical | ChemComp-MN / #3: Chemical | ChemComp-GAI / #4: 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: 2.67 Å3/Da / Density % sol: 54 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 8.5 Details: HANGING DROP VAPOUR DIFFUSION, MIXING 2 UL PROTEIN WITH 2 UL RESERVOIR SOLUTION. PROTEIN SOLUTION 27 MG/ML PROTEIN, 10 MM MOPS,PH 7.5. RESERVOIR SOLUTION 27-30% MONOMETHYLPEG 5000, 10 MM ...Details: HANGING DROP VAPOUR DIFFUSION, MIXING 2 UL PROTEIN WITH 2 UL RESERVOIR SOLUTION. PROTEIN SOLUTION 27 MG/ML PROTEIN, 10 MM MOPS,PH 7.5. RESERVOIR SOLUTION 27-30% MONOMETHYLPEG 5000, 10 MM MNCL2, 10 MM GUANIDINE HYDROCHLORIDE, IN 0.1 M BISTRISPROPANE/HCL, PH 8.5., VAPOR DIFFUSION, HANGING DROP | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 113 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Dec 15, 1996 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→40 Å / Num. obs: 93307 / % possible obs: 87.9 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 15.4 |
Reflection shell | Resolution: 2.15→2.3 Å / Rmerge(I) obs: 0.271 / Mean I/σ(I) obs: 3.1 / % possible all: 63.2 |
Reflection | *PLUS Num. measured all: 436708 |
Reflection shell | *PLUS % possible obs: 63.2 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: LOW RESOLUTION STRUCTURE OF A DIFFERENT CRYSTAL FORM Resolution: 2.15→6 Å / Isotropic thermal model: INDIVIDUAL ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0
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Refine analyze | Luzzati d res low obs: 6 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.15→6 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: RESTRAINTS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file | Serial no: 1 / Param file: PARAM19X.PRO / Topol file: TOPH19X.PRO | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.195 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |