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Yorodumi- PDB-3t41: 1.95 Angstrom Resolution Crystal Structure of Epidermin Leader Pe... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3t41 | ||||||
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Title | 1.95 Angstrom Resolution Crystal Structure of Epidermin Leader Peptide Processing Serine Protease (EpiP) S393A Mutant from Staphylococcus aureus | ||||||
Components | Epidermin leader peptide processing serine protease EpiP | ||||||
Keywords | HYDROLASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / Alpha and beta proteins (a/b) / Subtilisin-like / Rossmann fold / serine-type endopeptidase activity | ||||||
Function / homology | Function and homology information Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / serine-type endopeptidase activity / proteolysis / metal ion binding Similarity search - Function | ||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Minasov, G. / Kuhn, M. / Ruan, J. / Halavaty, A. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Bagnoli, F. / Falugi, F. / Bottomley, M. ...Minasov, G. / Kuhn, M. / Ruan, J. / Halavaty, A. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Bagnoli, F. / Falugi, F. / Bottomley, M. / Grandi, G. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Citation | Journal: TO BE PUBLISHED Title: 1.95 Angstrom Resolution Crystal Structure of Epidermin Leader Peptide Processing Serine Protease (EpiP) S393A Mutant from Staphylococcus aureus. Authors: Minasov, G. / Kuhn, M. / Ruan, J. / Halavaty, A. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Bagnoli, F. / Falugi, F. / Bottomley, M. / Grandi, G. / Anderson, W.F. / Center for Structural ...Authors: Minasov, G. / Kuhn, M. / Ruan, J. / Halavaty, A. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Bagnoli, F. / Falugi, F. / Bottomley, M. / Grandi, G. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3t41.cif.gz | 376.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3t41.ent.gz | 307.9 KB | Display | PDB format |
PDBx/mmJSON format | 3t41.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3t41_validation.pdf.gz | 449.7 KB | Display | wwPDB validaton report |
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Full document | 3t41_full_validation.pdf.gz | 460.4 KB | Display | |
Data in XML | 3t41_validation.xml.gz | 36.2 KB | Display | |
Data in CIF | 3t41_validation.cif.gz | 53.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t4/3t41 ftp://data.pdbj.org/pub/pdb/validation_reports/t4/3t41 | HTTPS FTP |
-Related structure data
Related structure data | 3qfhS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 52700.789 Da / Num. of mol.: 2 / Fragment: sequence database residues 28-457 / Mutation: S393A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: COL / Gene: epiP, SACOL1874 / Plasmid: pET 15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic References: UniProt: Q5HEV5, UniProt: A0A0H2WX20*PLUS, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases #2: Chemical | ChemComp-CA / #3: Chemical | ChemComp-CL / | #4: 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: 2.26 Å3/Da / Density % sol: 45.58 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8 Details: Protein solution: 7.8 mG/mL, 0.25M Sodium chloride, 0.01M Tris HCl (pH 8.3), Screen solution: PACT (D11), 0.2M Calcium chloride, 0.1M Tris (pH 8.0), 20% w/v PEG 6000, VAPOR DIFFUSION, ...Details: Protein solution: 7.8 mG/mL, 0.25M Sodium chloride, 0.01M Tris HCl (pH 8.3), Screen solution: PACT (D11), 0.2M Calcium chloride, 0.1M Tris (pH 8.0), 20% w/v PEG 6000, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 21, 2011 / Details: Beryllium lenses |
Radiation | Monochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→30 Å / Num. all: 67885 / Num. obs: 67885 / % possible obs: 98 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 32.7 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 25.5 |
Reflection shell | Resolution: 1.95→1.98 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.473 / Mean I/σ(I) obs: 3 / Num. unique all: 3419 / % possible all: 97.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3QFH Resolution: 1.95→29.94 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.959 / SU B: 7.083 / SU ML: 0.092 Isotropic thermal model: Atomic Thermal Factors Individually Refined Cross valid method: THROUGHOUT / ESU R: 0.153 / ESU R Free: 0.132 / 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: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.031 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→29.94 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2 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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