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Yorodumi- PDB-4hx2: Crystal structure of Streptomyces caespitosus sermetstatin in com... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4hx2 | ||||||
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Title | Crystal structure of Streptomyces caespitosus sermetstatin in complex with Bacillus licheniformis subtilisin | ||||||
Components |
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Keywords | Hydrolase/Hydrolase Inhibitor / Streptomyces subtilisin inhibitor fold / Subtilisin Carlsberg / Hydrolase-Hydrolase Inhibitor complex | ||||||
Function / homology | Function and homology information serine-type endopeptidase inhibitor activity / serine-type endopeptidase activity / proteolysis / extracellular space / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | Streptomyces caespitosus (bacteria) Bacillus licheniformis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | ||||||
Authors | Trillo-Muyo, S. / Martinez-Rodriguez, S. / Arolas, J.L. / Gomis-Ruth, F.X. | ||||||
Citation | Journal: CHEM SCI / Year: 2013 Title: Mechanism of action of a Janus-faced single-domain protein inhibitor simultaneously targeting two peptidase classes Authors: Trillo-Muyo, S. / Martinez-Rodriguez, S. / Arolas, J.L. / Gomis-Ruth, F.X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4hx2.cif.gz | 298.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4hx2.ent.gz | 240.9 KB | Display | PDB format |
PDBx/mmJSON format | 4hx2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hx/4hx2 ftp://data.pdbj.org/pub/pdb/validation_reports/hx/4hx2 | HTTPS FTP |
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-Related structure data
Related structure data | 4hwxSC 4hx3C 1sbcS 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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Unit cell |
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Details | dimer of dimer |
-Components
-Protein , 2 types, 4 molecules ACBD
#1: Protein | Mass: 27306.199 Da / Num. of mol.: 2 / Fragment: Mature protease / Source method: isolated from a natural source / Source: (natural) Bacillus licheniformis (bacteria) / References: UniProt: Q9FDF2, subtilisin #2: Protein | Mass: 11923.354 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces caespitosus (bacteria) / Gene: ScNPI / Plasmid: pET32a / Production host: Escherichia coli (E. coli) / Strain (production host): Origami / References: UniProt: Q9FDS0 |
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-Non-polymers , 11 types, 377 molecules
#3: Chemical | ChemComp-CA / #4: Chemical | #5: Chemical | ChemComp-CL / | #6: Chemical | ChemComp-1AX / ( | #7: Chemical | ChemComp-PO4 / | #8: Chemical | #9: Chemical | #10: Chemical | #11: Chemical | ChemComp-CAC / | #12: Chemical | ChemComp-ACT / | #13: 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: 3.56 Å3/Da / Density % sol: 65.42 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1 M cacodylate, 0.2 M zinc acetate dihydrate, 10% (v/v) 2-propanol, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9763 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 25, 2010 |
Radiation | Monochromator: Si(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→48.6 Å / Num. all: 52346 / Num. obs: 52346 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 44.11 Å2 / Rmerge(I) obs: 0.097 / Net I/σ(I): 13.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1SBC, 4HWX Resolution: 2.25→32.94 Å / Cor.coef. Fo:Fc: 0.9296 / Cor.coef. Fo:Fc free: 0.9143 / SU R Cruickshank DPI: 0.18 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 51.65 Å2
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Refine analyze | Luzzati coordinate error obs: 0.326 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.25→32.94 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.25→2.31 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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