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Open data
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Basic information
Entry | Database: PDB / ID: 3cev | ||||||
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Title | ARGINASE FROM BACILLUS CALDEVELOX, COMPLEXED WITH L-ARGININE | ||||||
![]() | PROTEIN (ARGINASE) | ||||||
![]() | HYDROLASE / ENZYME / ARGININE HYDROLYSIS / NITROGEN METABOLISM / MANGANESE METALLOENZYME | ||||||
Function / homology | ![]() arginase / arginase activity / arginine catabolic process to ornithine / urea cycle / manganese ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Bewley, M.C. / Jeffrey, P.D. / Patchett, M.L. / Kanyo, Z.F. / Baker, E.N. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 355.5 KB | Display | ![]() |
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PDB format | ![]() | 290.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 412.4 KB | Display | ![]() |
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Full document | ![]() | 428.2 KB | Display | |
Data in XML | ![]() | 35.3 KB | Display | |
Data in CIF | ![]() | 56.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1cevC ![]() 2cevSC ![]() 4cevC ![]() 5cevC 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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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 Details: STRUCTURE CONTAINS TWO ARGININE LIGANDS BOUND TO EACH MOLECULE. ONE (LABELLED R 407 - R 412) IS BOUND IN THE ACTIVE SITE, COORDINATED TO THE SINGLE MN. THE OTHER (LABELLED R 401 - R 406) IS ...Details: STRUCTURE CONTAINS TWO ARGININE LIGANDS BOUND TO EACH MOLECULE. ONE (LABELLED R 407 - R 412) IS BOUND IN THE ACTIVE SITE, COORDINATED TO THE SINGLE MN. THE OTHER (LABELLED R 401 - R 406) IS AT AN EXTERNAL SITE, BETWEEN SUBUNITS. EACH MOLECULE HAS JUST A SINGLE MN ION AT THE ACTIVE SITE (MNA) INSTEAD OF THE USUAL TWO. THE SECOND WAS REMOVED BY TREATMENT WITH EDTA. Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-MN / #3: Chemical | ChemComp-ARG / #4: Water | ChemComp-HOH / | Nonpolymer details | TWO ARGININE LIGANDS ARE BOUND TO EACH MOLECULE, ONE AT THE ACTIVE SITE, THE OTHER AT AN ...TWO ARGININE LIGANDS ARE BOUND TO EACH MOLECULE, ONE AT THE ACTIVE SITE, THE OTHER AT AN INTERMOLEC | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: MIXING 2 UL PROTEIN WITH 2 UL RESERVOIR SOLUTION PROTEIN SOLUTION 27 MG/ML PROTEIN, 10 MM MOPS,PH 7.5 RESERVOIR SOLUTION 28% MONOMETHYLPEG 2000, 10 MM EDTA, 10 MM GUANIDINE HYDROCHLORIDE, IN ...Details: MIXING 2 UL PROTEIN WITH 2 UL RESERVOIR SOLUTION PROTEIN SOLUTION 27 MG/ML PROTEIN, 10 MM MOPS,PH 7.5 RESERVOIR SOLUTION 28% MONOMETHYLPEG 2000, 10 MM EDTA, 10 MM GUANIDINE HYDROCHLORIDE, IN 0.05 M BISTRISPROPANE/HCL, PH 8. THE CRYSTALS WERE THEN SOAKED IN 42.5% MMPEG 2000, 10 MM GUANIDINE HYDROCHLORIDE, 10 MM L-ARGININE, 10 MM EDTA, 0.05M BISTRISPROPANE/HCL, PH 8.5 FOR 8 HOURS, 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: ![]() |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Jan 1, 1997 |
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: 2.4→40 Å / Num. obs: 73511 / % possible obs: 89.7 % / Redundancy: 2.75 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 14.1 |
Reflection shell | Resolution: 2.4→2.55 Å / Rmerge(I) obs: 0.169 / Mean I/σ(I) obs: 3.8 / % possible all: 52.4 |
Reflection | *PLUS Lowest resolution: 50 Å / Num. measured all: 201956 |
Reflection shell | *PLUS % possible obs: 52.4 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: REFINED MODEL FOR THE PH 8.5 NATIVE STRUCTURE: 2CEV Resolution: 2.4→8 Å / Isotropic thermal model: INDIVIDUAL ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0
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Refine analyze | Luzzati d res low obs: 8 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→8 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: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.193 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |