+Open data
-Basic information
Entry | Database: PDB / ID: 1okx | ||||||
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Title | Binding Structure of Elastase Inhibitor Scyptolin A | ||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR / PROTEASE / ELASTASE / INHIBITOR / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR COMPLEX | ||||||
Function / homology | Function and homology information pancreatic elastase / serine-type endopeptidase activity / proteolysis / extracellular space / metal ion binding Similarity search - Function | ||||||
Biological species | SUS SCROFA (pig) SCYTONEMA HOFMANNI (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Matern, U. / Schleberger, C. / Jelakovic, S. / Weckesser, J. / Schulz, G.E. | ||||||
Citation | Journal: Chem.Biol. / Year: 2003 Title: Binding Structure of Elastase Inhibitor Scyptolin A Authors: Matern, U. / Schleberger, C. / Jelakovic, S. / Weckesser, J. / Schulz, G.E. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1okx.cif.gz | 103.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1okx.ent.gz | 80.5 KB | Display | PDB format |
PDBx/mmJSON format | 1okx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1okx_validation.pdf.gz | 443.3 KB | Display | wwPDB validaton report |
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Full document | 1okx_full_validation.pdf.gz | 452.9 KB | Display | |
Data in XML | 1okx_validation.xml.gz | 20.9 KB | Display | |
Data in CIF | 1okx_validation.cif.gz | 28.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ok/1okx ftp://data.pdbj.org/pub/pdb/validation_reports/ok/1okx | HTTPS FTP |
-Related structure data
Related structure data | 1elbS S: Starting model for refinement |
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Similar 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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.914185, -0.335757, 0.227008), Vector: |
-Components
#1: Protein | Mass: 25928.031 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: PANCREAS / References: UniProt: P00772, pancreatic elastase #2: Protein/peptide | #3: Water | ChemComp-HOH / | Compound details | CATALYTIC ACTIVITY: HYDROLYSIS | |
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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: 3.18 Å3/Da / Density % sol: 61 % | ||||||||||||||||||||||||
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Crystal grow | pH: 5 / Details: PH 5.00 | ||||||||||||||||||||||||
Crystal grow | *PLUS pH: 5 / 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 RU200B / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→19.29 Å / Num. obs: 16453 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 8.3 % / Biso Wilson estimate: 6.2 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 13.6 |
Reflection shell | Resolution: 2.8→2.86 Å / Redundancy: 8.4 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 5.5 / % possible all: 100 |
Reflection | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 30 Å / % possible obs: 99 % / Redundancy: 8.3 % / Rmerge(I) obs: 0.133 |
Reflection shell | *PLUS % possible obs: 100 % / Redundancy: 8.4 % / Num. unique obs: 999 / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 5.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1ELB Resolution: 2.8→19.29 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 5269536.9 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 28.37 Å2 / ksol: 0.39 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.8→19.29 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.98 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS % reflection Rfree: 10 % / Rfactor Rfree: 0.258 / Rfactor Rwork: 0.209 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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