+Open data
-Basic information
Entry | Database: PDB / ID: 3cev | ||||||
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Title | ARGINASE FROM BACILLUS CALDEVELOX, COMPLEXED WITH L-ARGININE | ||||||
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: 2.4 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 | 3cev.cif.gz | 355.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3cev.ent.gz | 290.5 KB | Display | PDB format |
PDBx/mmJSON format | 3cev.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3cev_validation.pdf.gz | 412.4 KB | Display | wwPDB validaton report |
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Full document | 3cev_full_validation.pdf.gz | 428.2 KB | Display | |
Data in XML | 3cev_validation.xml.gz | 35.3 KB | Display | |
Data in CIF | 3cev_validation.cif.gz | 56.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ce/3cev ftp://data.pdbj.org/pub/pdb/validation_reports/ce/3cev | HTTPS FTP |
-Related structure data
Related structure data | 1cevC 2cevSC 4cevC 5cevC S: Starting model for refinement C: citing same article (ref.) |
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Similar 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 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.) Bacillus caldovelox (bacteria) / Strain: BACILLUS SPECIES DSM 411 / Description: 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-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: 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: 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: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
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 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.193 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |