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Yorodumi- PDB-6nfp: 1.7 Angstrom Resolution Crystal Structure of Arginase from Bacill... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6nfp | |||||||||
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Title | 1.7 Angstrom Resolution Crystal Structure of Arginase from Bacillus subtilis subsp. subtilis str. 168 | |||||||||
Components | Arginase | |||||||||
Keywords | HYDROLASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID | |||||||||
Function / homology | Function and homology information arginine metabolic process / arginine catabolic process to ornithine / arginase / arginase activity / urea cycle / manganese ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Bacillus subtilis (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | |||||||||
Authors | Minasov, G. / Wawrzak, Z. / Evdokimova, E. / Grimshaw, S. / Kwon, K. / Savchenko, A. / Satchell, K.J.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID) | |||||||||
Citation | Journal: To Be Published Title: 1.7 Angstrom Resolution Crystal Structure of Arginase from Bacillus subtilis subsp. subtilis str. 168 Authors: Minasov, G. / Wawrzak, Z. / Evdokimova, E. / Grimshaw, S. / Kwon, K. / Savchenko, A. / Satchell, K.J.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID) | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6nfp.cif.gz | 708.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6nfp.ent.gz | 584 KB | Display | PDB format |
PDBx/mmJSON format | 6nfp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nf/6nfp ftp://data.pdbj.org/pub/pdb/validation_reports/nf/6nfp | HTTPS FTP |
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-Related structure data
Related structure data | 2cevS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 6 molecules ABCDEF
#1: Protein | Mass: 32466.064 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria) Strain: 168 / Gene: rocF, BSU40320, argI / Plasmid: pMCSG53 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) Strain (production host): BL21 DE3 gold magic / References: UniProt: P39138, arginase |
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-Non-polymers , 10 types, 1717 molecules
#2: Chemical | ChemComp-CL / #3: Chemical | #4: Chemical | ChemComp-MG / #5: Chemical | ChemComp-FMT / #6: Chemical | ChemComp-URE / #7: Chemical | ChemComp-EDO / #8: Chemical | ChemComp-SO4 / #9: Chemical | #10: Chemical | ChemComp-GOA / #11: 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: 2.34 Å3/Da / Density % sol: 47.4 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: Protein: 40.0 mg/ml, 0.3M Sodium chloride, 0.01M HEPES pH 7.5, Screen: 0.2M Magnesium chloride,0.1M Tris-HCL pH 8.5, 17% (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 23, 2017 / Details: C(111) |
Radiation | Monochromator: Be / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→30 Å / Num. obs: 191464 / % possible obs: 94.5 % / Observed criterion σ(I): -3 / Redundancy: 4.4 % / Biso Wilson estimate: 27.1 Å2 / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.032 / Rrim(I) all: 0.069 / Rsym value: 0.061 / Χ2: 1.026 / Net I/σ(I): 20.3 |
Reflection shell | Resolution: 1.7→1.73 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.779 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 9654 / CC1/2: 0.618 / Rpim(I) all: 0.421 / Rrim(I) all: 0.887 / Rsym value: 0.779 / Χ2: 1.028 / % possible all: 95.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2CEV Resolution: 1.7→29.99 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.97 / SU B: 3.582 / SU ML: 0.057 / Cross valid method: THROUGHOUT / ESU R: 0.089 / ESU R Free: 0.086 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.936 Å2
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Refinement step | Cycle: 1 / Resolution: 1.7→29.99 Å
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Refine LS restraints |
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