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Yorodumi- PDB-3qh1: Structure of Thermolysin in complex with N-benzyloxycarbonyl-L-as... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3qh1 | ||||||
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Title | Structure of Thermolysin in complex with N-benzyloxycarbonyl-L-aspartic acid | ||||||
Components | Thermolysin | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / HYDROLASE / METALLOPROTEINASE / N-benzyloxycarbonyl-L-aspartic acid / 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: 1.55 Å | ||||||
Authors | Birrane, G. / Bhyravbhatla, B. / Navia, M. | ||||||
Citation | Journal: ACS MED.CHEM.LETT. / Year: 2014 Title: Synthesis of Aspartame by Thermolysin: An X-ray Structural Study. Authors: Birrane, G. / Bhyravbhatla, B. / Navia, M.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3qh1.cif.gz | 157.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3qh1.ent.gz | 124.1 KB | Display | PDB format |
PDBx/mmJSON format | 3qh1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3qh1_validation.pdf.gz | 760.8 KB | Display | wwPDB validaton report |
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Full document | 3qh1_full_validation.pdf.gz | 761.8 KB | Display | |
Data in XML | 3qh1_validation.xml.gz | 17.9 KB | Display | |
Data in CIF | 3qh1_validation.cif.gz | 28.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qh/3qh1 ftp://data.pdbj.org/pub/pdb/validation_reports/qh/3qh1 | HTTPS FTP |
-Related structure data
Related structure data | 3qgoC 3qh5C 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
#1: Protein | Mass: 34360.336 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus thermoproteolyticus (bacteria) / References: UniProt: P00800, thermolysin | ||||||
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#2: Chemical | ChemComp-CA / #3: Chemical | ChemComp-ZN / | #4: Chemical | ChemComp-NX6 / | #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: 2.34 Å3/Da / Density % sol: 47.4 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: THERMOLYSIN WAS DISSOLVED IN 30% DMSO, 36mM TRIS/HCl, 1M CALCIUM ACETATE pH 6.3 AT 100MG/ML, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.075 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 3, 2010 |
Radiation | Monochromator: SAGITALLY FOCUSED Si(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.075 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→100 Å / Num. all: 48259 / Num. obs: 48259 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 19.4 % / Biso Wilson estimate: 19.3 Å2 / Rmerge(I) obs: 0.087 / Rsym value: 0.107 / Net I/σ(I): 27.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 8TLN Resolution: 1.55→34.11 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.976 / SU B: 2.142 / SU ML: 0.035 / Cross valid method: THROUGHOUT / ESU R Free: 0.061 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.863 Å2
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Refinement step | Cycle: LAST / Resolution: 1.55→34.11 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.55→1.58 Å / Total num. of bins used: 20
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