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Yorodumi- PDB-2nu4: Accommodation of positively-charged residues in a hydrophobic spe... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2nu4 | ||||||
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Title | Accommodation of positively-charged residues in a hydrophobic specificity pocket: Crystal structures of SGPB in complex with OMTKY3 variants Lys18I and Arg18I | ||||||
Components |
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Keywords | HYDROLASE / ENZYME-INHIBITOR COMPLEX / CHARGED P1 RESIDUE | ||||||
Function / homology | Function and homology information streptogrisin B / molecular function inhibitor activity / serine-type endopeptidase inhibitor activity / serine-type endopeptidase activity / proteolysis / extracellular region Similarity search - Function | ||||||
Biological species | Meleagris gallopavo (turkey) Streptomyces griseus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MIR / Resolution: 1.75 Å | ||||||
Authors | Bateman, K.S. / Anderson, S. / Lu, W. / Qasim, M.A. / Laskowski Jr., M. / James, M.N.G. | ||||||
Citation | Journal: To be Published Title: Accommodation of positively-charged residues in a hydrophobic specificity pocket: Crystal structures of SGPB in complex with OMTKY3 variants Lys18I and Arg18I Authors: Bateman, K.S. / Anderson, S. / Lu, W. / Qasim, M.A. / Laskowski Jr., M. / James, M.N.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2nu4.cif.gz | 60.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2nu4.ent.gz | 42.1 KB | Display | PDB format |
PDBx/mmJSON format | 2nu4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2nu4_validation.pdf.gz | 417.4 KB | Display | wwPDB validaton report |
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Full document | 2nu4_full_validation.pdf.gz | 419.8 KB | Display | |
Data in XML | 2nu4_validation.xml.gz | 12.6 KB | Display | |
Data in CIF | 2nu4_validation.cif.gz | 17.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nu/2nu4 ftp://data.pdbj.org/pub/pdb/validation_reports/nu/2nu4 | HTTPS FTP |
-Related structure data
Related structure data | 2nu2C 2nu3C 3sgbS 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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-Components
#1: Protein | Mass: 18653.232 Da / Num. of mol.: 1 / Fragment: residues 115-299 / Source method: isolated from a natural source / Source: (natural) Streptomyces griseus (bacteria) / Strain: K1 / References: UniProt: P00777, streptogrisin B |
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#2: Protein | Mass: 5601.311 Da / Num. of mol.: 1 / Fragment: third domain, residues 135-185 / Mutation: L18K Source method: isolated from a genetically manipulated source Source: (gene. exp.) Meleagris gallopavo (turkey) / Plasmid: PEZZ318 / Production host: Escherichia coli (E. coli) / References: UniProt: P68390 |
#3: 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: 2.04 Å3/Da / Density % sol: 39.61 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: PEG 4000, SODIUM POTASSIUM PHOSPHATE at pH 7.1 24h before data collection, crystal was transferred to PEG4000, NaKHPO4 at pH 10.7, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54178 Å |
Detector | Type: MAC Science DIP-2030 / Detector: IMAGE PLATE / Date: Mar 28, 1998 / Details: mirrors |
Radiation | Monochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→20 Å / Num. all: 19840 / Num. obs: 19056 / % possible obs: 95.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 5 / Redundancy: 3.6 % / Rmerge(I) obs: 0.173 / Net I/σ(I): 8.59 |
Reflection shell | Resolution: 1.75→1.76 Å / Rmerge(I) obs: 0.359 / Mean I/σ(I) obs: 1.72 / % possible all: 70.4 |
-Processing
Software |
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Refinement | Method to determine structure: MIR Starting model: PDB ENTRY 3SGB Resolution: 1.75→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refine analyze | Luzzati coordinate error obs: 0.17 Å / Luzzati sigma a obs: 0.21 Å | |||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.75→20 Å
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Refine LS restraints |
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