+Open data
-Basic information
Entry | Database: PDB / ID: 4hwx | ||||||
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Title | Crystal structure of Streptomyces caespitosus sermetstatin | ||||||
Components | Neutral proteinase inhibitor ScNPI | ||||||
Keywords | Hydrolase Inhibitor / Streptomyces subtilisin inhibitor fold | ||||||
Function / homology | Function and homology information serine-type endopeptidase inhibitor activity / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | Streptomyces caespitosus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 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 | 4hwx.cif.gz | 54.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4hwx.ent.gz | 43 KB | Display | PDB format |
PDBx/mmJSON format | 4hwx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4hwx_validation.pdf.gz | 434.9 KB | Display | wwPDB validaton report |
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Full document | 4hwx_full_validation.pdf.gz | 434.8 KB | Display | |
Data in XML | 4hwx_validation.xml.gz | 8 KB | Display | |
Data in CIF | 4hwx_validation.cif.gz | 10.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hw/4hwx ftp://data.pdbj.org/pub/pdb/validation_reports/hw/4hwx | HTTPS FTP |
-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: 11923.354 Da / Num. of mol.: 1 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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#2: Chemical | ChemComp-GOL / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.2 Å3/Da / Density % sol: 61.58 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 0.1 M sodium citrate dihydrate, 0.2 M ammonium acetate, 10% (w/v) PEG3350, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 6, 2009 |
Radiation | Monochromator: Si(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→39.9 Å / Num. all: 12234 / Num. obs: 12234 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 34.43 Å2 / Rmerge(I) obs: 0.038 / Net I/σ(I): 40.3 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.9→39.89 Å / Cor.coef. Fo:Fc: 0.9437 / Cor.coef. Fo:Fc free: 0.9258 / SU R Cruickshank DPI: 0.122 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 42.28 Å2
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Refine analyze | Luzzati coordinate error obs: 0.273 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→39.89 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.08 Å / Total num. of bins used: 6
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Refinement TLS params. | Method: refined / Origin x: -3.4193 Å / Origin y: 25.3953 Å / Origin z: 2.1786 Å
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Refinement TLS group | Selection details: { A|* } |