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Yorodumi- PDB-3co0: Substrate Complex of Fluoride-sensitive Engineered Subtilisin SUB... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3co0 | ||||||
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Title | Substrate Complex of Fluoride-sensitive Engineered Subtilisin SUBT_BACAM | ||||||
Components | (Subtilisin BPN') x 2 | ||||||
Keywords | HYDROLASE / fluoride activated protease / anion sensor / Metal-binding / Secreted / Serine protease / Sporulation / Zymogen | ||||||
Function / homology | Function and homology information subtilisin / sporulation resulting in formation of a cellular spore / fibrinolysis / serine-type endopeptidase activity / proteolysis / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | Bacillus amyloliquefaciens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.93 Å | ||||||
Authors | Gallagher, D.T. / Bryan, P.N. | ||||||
Citation | Journal: Biochemistry / Year: 2009 Title: Structure of a switchable subtilisin complexed with a substrate and with the activator azide. Authors: Gallagher, T. / Ruan, B. / London, M. / Bryan, M.A. / Bryan, P.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3co0.cif.gz | 79.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3co0.ent.gz | 60.8 KB | Display | PDB format |
PDBx/mmJSON format | 3co0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/co/3co0 ftp://data.pdbj.org/pub/pdb/validation_reports/co/3co0 | HTTPS FTP |
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-Related 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: 8786.066 Da / Num. of mol.: 1 / Fragment: Prodomain Mutation: K27E, V37L, Q40C, K57E, H72K, V73L, A74Y, H75R, Y77L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus amyloliquefaciens (bacteria) / Gene: apr / Production host: Escherichia coli (E. coli) / References: UniProt: P00782 | ||||
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#2: Protein | Mass: 26420.447 Da / Num. of mol.: 1 / Fragment: Enzyme domain Mutation: Q2K, S3C, P5S, S9A, I31L, D32A, K43N, M50F, A73L, Y104A, G128S, E156S, G166S, G169A, S188P, Q206C, N212G, K217L, N218S, S221A, T254A, Q271E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus amyloliquefaciens (bacteria) / Gene: apr / Production host: Escherichia coli (E. coli) / References: UniProt: P00782, subtilisin | ||||
#3: Chemical | ChemComp-ZN / #4: Water | ChemComp-HOH / | Sequence details | AUTHOR STATES THAT RESIDUES 17-23 TMSTMSA WAS REPLACED WITH GFKSC | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.12 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 20 mg/mL ptn, l8% PEG8K, 0.2M ZnAc, 0.1M Cacodylate, pH 6.5, vapor diffusion, hanging drop, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAXIS / Detector: IMAGE PLATE / Date: Apr 1, 2007 / Details: mirrors | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: coated mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Redundancy: 4.42 % / Av σ(I) over netI: 16.8 / Number: 130517 / Rmerge(I) obs: 0.059 / Χ2: 0.97 / D res high: 1.8 Å / D res low: 19.96 Å / Num. obs: 29275 / % possible obs: 99.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell | ID: 1
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Reflection | Resolution: 1.8→19.96 Å / Num. all: 29275 / Num. obs: 29275 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.42 % / Rmerge(I) obs: 0.059 / Χ2: 0.97 / Net I/σ(I): 16.8 / Scaling rejects: 980 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Resolution: 1.93→8 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.874 / SU B: 4.595 / SU ML: 0.137 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.216 / ESU R Free: 0.197 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.128 Å2
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Refinement step | Cycle: LAST / Resolution: 1.93→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.93→1.977 Å / Total num. of bins used: 20
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