+Open data
-Basic information
Entry | Database: PDB / ID: 1oss | ||||||
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Title | T190P STREPTOMYCES GRISEUS TRYPSIN IN COMPLEX WITH BENZAMIDINE | ||||||
Components | trypsin | ||||||
Keywords | HYDROLASE / TRYPSIN / SERINE PROTEASE / MUTANT | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptomyces griseus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / RIGID BODY REFINEMENT / Resolution: 1.93 Å | ||||||
Authors | Page, M.J. / Wong, S.L. / Hewitt, J. / Strynadka, N.C. / MacGillivray, R.T. | ||||||
Citation | Journal: Biochemistry / Year: 2003 Title: Engineering the Primary Substrate Specificity of Streptomyces griseus Trypsin. Authors: Page, M.J. / Wong, S.L. / Hewitt, J. / Strynadka, N.C. / MacGillivray, R.T. #1: Journal: J.Mol.Biol. / Year: 1988 Title: Refined Crystal Structure of Streptomyces Griseus Trypsin at 1.7 Angstroms Resolution Authors: Read, R.J. / James, M.N.G. #2: Journal: Biochemistry / Year: 1984 Title: Critical Comparison of Comparative Model Building of Streptomyces Griseus Trypsin Authors: Read, R.J. / Brayer, G.D. / Jurasek, L. / James, M.N.G. | ||||||
History |
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Remark 999 | SEQUENCE AMINO ACID NUMBERING IS BASED ON CHYMOTRYPSINOGEN AND IS THE SAME AS THAT USED IN THE ...SEQUENCE AMINO ACID NUMBERING IS BASED ON CHYMOTRYPSINOGEN AND IS THE SAME AS THAT USED IN THE NATIVE STRUCTURE (PDB ID 1SGT). |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1oss.cif.gz | 61 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1oss.ent.gz | 42.9 KB | Display | PDB format |
PDBx/mmJSON format | 1oss.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/os/1oss ftp://data.pdbj.org/pub/pdb/validation_reports/os/1oss | HTTPS FTP |
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-Related structure data
Related structure data | 1os8C 1sgtS 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: 23118.799 Da / Num. of mol.: 1 / Mutation: T190P Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces griseus (bacteria) / Gene: SPRT / Plasmid: PWB980 / Production host: Bacillus subtilis (bacteria) / Strain (production host): WB700 / References: UniProt: P00775, trypsin | ||||||
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#2: Chemical | #3: Chemical | ChemComp-CA / | #4: Chemical | ChemComp-BEN / | #5: 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: 2.02 Å3/Da / Density % sol: 38.7 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 1.55 M AMMONIUM SULPHATE, 10 MM CALCIUM ACETATE , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 6.2 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 21, 2002 |
Radiation | Monochromator: OSMIC MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.93→20 Å / Num. obs: 16130 / % possible obs: 89.7 % / Observed criterion σ(I): 2 / Biso Wilson estimate: 7.1 Å2 / Rmerge(I) obs: 0.031 |
Reflection shell | Resolution: 1.93→2 Å / Rmerge(I) obs: 0.056 / % possible all: 79.1 |
Reflection | *PLUS Highest resolution: 1.9 Å / Num. obs: 14471 |
Reflection shell | *PLUS Lowest resolution: 2.05 Å / % possible obs: 79.1 % / Mean I/σ(I) obs: 25.2 |
-Processing
Software |
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Refinement | Method to determine structure: RIGID BODY REFINEMENT Starting model: 1SGT Resolution: 1.93→19.86 Å / Rfactor Rfree error: 0.008 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: RESIDUES 165 AND 192 HAVE TWO ALTERNATE CONFORMATIONS THAT ARE CLEARLY VISIBLE IN THE ELECTRON DENSITY
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 56.6589 Å2 / ksol: 0.442522 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.8 Å2
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Refine analyze | Luzzati coordinate error free: 0.23 Å / Luzzati sigma a free: 0.12 Å | ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.93→19.86 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.93→2.05 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: XTALVIEW / Classification: refinement | ||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.9 Å | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.2 |