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Yorodumi- PDB-1tk2: Crystal Structure of the Complex formed between Alkaline Proteina... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1tk2 | ||||||
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Title | Crystal Structure of the Complex formed between Alkaline Proteinase Savinase and Gramicidin S at 1.5A Resolution | ||||||
Components |
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Keywords | HYDROLASE/ANTIBIOTIC / GRAMICIDIN / ANTIBIOTIC / ANTIFUNGAL / ANTIBACTERIAL / CYCLIC GRAMICIDIN / MEMBRANE ION CHANNEL / HYDROLASE-ANTIBIOTIC COMPLEX | ||||||
Function / homology | Function and homology information subtilisin / sporulation resulting in formation of a cellular spore / serine-type endopeptidase activity / proteolysis / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | BACILLUS LENTUS (bacteria) BREVIBACILLUS BREVIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 Å | ||||||
Authors | Bhatt, V.S. / Kaur, P. / Klupsch, S. / Betzel, C. / Brenner, S. / Singh, T.P. | ||||||
Citation | Journal: To be Published Title: Crystal Structure of the Complex Formed between Alkaline Proteinase Savinase and Gramicidin S at 1.5A Resolution. Authors: Bhatt, V.S. / Kaur, P. / Klupsch, S. / Betzel, C. / Brenner, S. / Singh, T.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1tk2.cif.gz | 69.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1tk2.ent.gz | 49.7 KB | Display | PDB format |
PDBx/mmJSON format | 1tk2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1tk2_validation.pdf.gz | 375.6 KB | Display | wwPDB validaton report |
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Full document | 1tk2_full_validation.pdf.gz | 383 KB | Display | |
Data in XML | 1tk2_validation.xml.gz | 8.3 KB | Display | |
Data in CIF | 1tk2_validation.cif.gz | 12.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tk/1tk2 ftp://data.pdbj.org/pub/pdb/validation_reports/tk/1tk2 | HTTPS FTP |
-Related structure data
Related structure data | 1svnS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological Unit is Monomer |
-Components
#1: Protein | Mass: 26718.381 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) BACILLUS LENTUS (bacteria) / References: UniProt: P29600, subtilisin | ||||
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#2: Protein/peptide | Type: Cyclic peptide / Class: Antibiotic / Mass: 1159.461 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: GRAMICIDIN S IS A DECAPEPTIDE, RESIDUES 1 AND 10 FORM A PEPTIDE BOND RESULTING IN CYCLIZATION. Source: (synth.) BREVIBACILLUS BREVIS (bacteria) / References: NOR: NOR00249, GRAMICIDIN S | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Compound details | GRAMICIDIN S IS A CYCLODECAPEPTIDE, CONSTRUCTED AS TWO IDENTICAL PENTAPEPTIDES JOINED HEAD TO TAIL, ...GRAMICIDIN | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 35.8 % |
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Crystal grow | pH: 6.5 Details: 0.33M NACL, 10% PEG 4000, PH 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K |
-Data collection
Diffraction | Mean temperature: 277 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 1.009 |
Detector | Type: CUSTOM-MADE / Detector: OSCILLATION CAMERA / Date: Aug 17, 1991 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.009 Å / Relative weight: 1 |
Reflection | Num. obs: 31702 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1SVN Resolution: 1.54→27.32 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.948 / SU B: 1.679 / SU ML: 0.062 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.081 / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.93 Å2
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Refine analyze | Luzzati coordinate error obs: 0.157 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.54→27.32 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.54→1.58 Å / Total num. of bins used: 20 /
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