+Open data
-Basic information
Entry | Database: PDB / ID: 4mxj | ||||||
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Title | Thermolysin in complex with UBTLN35 | ||||||
Components | Thermolysin | ||||||
Keywords | hydrolase/hydrolase inhibitor / PROTEASE / METALLOPROTEASE / HYDROLYSIS OF PEPTIDE BONDS / 2-PHOSPHORAMIDON / HYDROLASE-HYDROLASE INHIBITOR COMPLEX | ||||||
Function / homology | Function and homology information thermolysin / metalloendopeptidase activity / proteolysis / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | Bacillus thermoproteolyticus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.349 Å | ||||||
Authors | Krimmer, S.G. / Heine, A. / Klebe, G. | ||||||
Citation | Journal: Chemmedchem / Year: 2014 Title: Methyl, Ethyl, Propyl, Butyl: Futile But Not for Water, as the Correlation of Structure and Thermodynamic Signature Shows in a Congeneric Series of Thermolysin Inhibitors. Authors: Krimmer, S.G. / Betz, M. / Heine, A. / Klebe, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4mxj.cif.gz | 163.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4mxj.ent.gz | 126.3 KB | Display | PDB format |
PDBx/mmJSON format | 4mxj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mx/4mxj ftp://data.pdbj.org/pub/pdb/validation_reports/mx/4mxj | HTTPS FTP |
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-Related structure data
Related structure data | 4mtwC 4mwpC 4mznC 4n4eC 4n5pC 4n66C 4oi5C 8tlnS C: citing same article (ref.) 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
-Protein , 1 types, 1 molecules E
#1: Protein | Mass: 34360.336 Da / Num. of mol.: 1 / Fragment: Mature form (UNP residues 233-548) / Source method: isolated from a natural source / Source: (natural) Bacillus thermoproteolyticus (bacteria) / References: UniProt: P00800, thermolysin |
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-Non-polymers , 6 types, 475 molecules
#2: Chemical | ChemComp-ZN / | ||||||||
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#3: Chemical | ChemComp-CA / #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-2G8 / | #7: 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: 2.35 Å3/Da / Density % sol: 47.74 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 50 mM Tris/HCl, 1.9 M CsCl, 50% DMSO, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291.15K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 26, 2012 / Details: Mirror |
Radiation | Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→50 Å / Num. obs: 70475 / % possible obs: 96.4 % / Redundancy: 4.7 % / Biso Wilson estimate: 9.654 Å2 / Rsym value: 0.069 / Net I/σ(I): 17.9 |
Reflection shell | Resolution: 1.35→1.37 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 3.8 / Num. unique all: 3410 / Rsym value: 0.475 / % possible all: 95.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 8TLN Resolution: 1.349→21.905 Å / SU ML: 0.1 / Cross valid method: R-free / σ(F): 1.35 / Phase error: 12.85 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.349→21.905 Å
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Refine LS restraints |
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LS refinement shell |
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