+Open data
-Basic information
Entry | Database: PDB / ID: 5cev | ||||||||||||
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Title | ARGINASE FROM BACILLUS CALDEVELOX, L-LYSINE COMPLEX | ||||||||||||
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: 2.5 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 | 5cev.cif.gz | 347.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5cev.ent.gz | 284.2 KB | Display | PDB format |
PDBx/mmJSON format | 5cev.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5cev_validation.pdf.gz | 424.5 KB | Display | wwPDB validaton report |
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Full document | 5cev_full_validation.pdf.gz | 441.5 KB | Display | |
Data in XML | 5cev_validation.xml.gz | 35.5 KB | Display | |
Data in CIF | 5cev_validation.cif.gz | 55.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ce/5cev ftp://data.pdbj.org/pub/pdb/validation_reports/ce/5cev | HTTPS FTP |
-Related structure data
Related structure data | 1cevC 2cevSC 3cevC 4cevC 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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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: EACH MOLECULE HAS AN L-LYSINE MOLECULE BOUND IN ITS ACTIVE SITE (THESE ARE LABELLED R 401 - R 406) AND A GUANIDINE ION AT AN EXTERNAL, INTER-SUBUNIT SITE (LABELLED R 407 - R 412). 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-LYS / #4: Chemical | ChemComp-GAI / #5: 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: 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, 5 MM MNCL2, 10 MM GUANIDINE HYDROCHLORIDE, ...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, 5 MM MNCL2, 10 MM GUANIDINE HYDROCHLORIDE, 10 MM L-LYSINE, IN 0.05 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: 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: 2.5→50 Å / Num. obs: 68127 / % possible obs: 94.9 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 18 |
Reflection shell | Resolution: 2.5→2.7 Å / Rmerge(I) obs: 0.188 / Mean I/σ(I) obs: 4.8 / % possible all: 72.7 |
Reflection | *PLUS Num. measured all: 424670 |
Reflection shell | *PLUS % possible obs: 72.7 % |
-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: 2.5→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: 2.5→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: 0.212 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |