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Yorodumi- PDB-1ifg: CRYSTAL STRUCTURE OF A MONOMERIC FORM OF GENERAL PROTEASE INHIBIT... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ifg | ||||||
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Title | CRYSTAL STRUCTURE OF A MONOMERIC FORM OF GENERAL PROTEASE INHIBITOR, ECOTIN IN ABSENCE OF A PROTEASE | ||||||
Components | ECOTIN | ||||||
Keywords | hydrolase inhibitor / monomeric ecotin / serine protease inhibitor | ||||||
Function / homology | Function and homology information serine-type endopeptidase inhibitor activity / outer membrane-bounded periplasmic space / protein homodimerization activity Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Eggers, C.T. / Wang, S.X. / Fletterick, R.J. / Craik, C.S. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2001 Title: The role of ecotin dimerization in protease inhibition. Authors: Eggers, C.T. / Wang, S.X. / Fletterick, R.J. / Craik, C.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ifg.cif.gz | 41.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ifg.ent.gz | 28 KB | Display | PDB format |
PDBx/mmJSON format | 1ifg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/if/1ifg ftp://data.pdbj.org/pub/pdb/validation_reports/if/1ifg | HTTPS FTP |
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-Related structure data
Related structure data | 1ecyS 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 15849.198 Da / Num. of mol.: 1 / Fragment: RESIDUES 26-162 OF ECOTIN PRECURSOR Mutation: INSERTION AFTER TRP130 THE SEQUENCE OF ALA-ASP-GLY Source method: isolated from a genetically manipulated source Details: MONOMERIC FORM / Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ECO OR ETI OR B2209 / Plasmid: PTACTAC / Production host: Escherichia coli (E. coli) / Strain (production host): JM101 / References: UniProt: P23827 |
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#2: 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: 2.77 Å3/Da / Density % sol: 55.67 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: PEG 4000, glycerol, Tris, Sodium Acetate, pH 8.0, VAPOR DIFFUSION, HANGING DROP at 298K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 200 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 1.08 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 15, 1999 / Details: mirrors |
Radiation | Monochromator: 0.87 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. all: 12036 / Num. obs: 11496 / % possible obs: 95.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 6 % / Biso Wilson estimate: 21.2 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 19 |
Reflection shell | Resolution: 1.98→2.02 Å / Redundancy: 6 % / Rmerge(I) obs: 0.472 / Mean I/σ(I) obs: 4.7 / Num. unique all: 835 / Rsym value: 0.472 / % possible all: 99.9 |
Reflection | *PLUS Num. measured all: 200193 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1ECY with last ten residues deleted Resolution: 2→19.92 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 593458.54 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 1
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 71.32 Å2 / ksol: 0.523 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→19.92 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 2 / % reflection Rfree: 10.2 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 42.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.284 / % reflection Rfree: 9.3 % / Rfactor Rwork: 0.271 |