+Open data
-Basic information
Entry | Database: PDB / ID: 6lzo | |||||||||
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Title | Thermolysin with 1,10-phenanthroline | |||||||||
Components | Thermolysin | |||||||||
Keywords | HYDROLASE / Thermolysin / metalloproteinase | |||||||||
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: 1.8 Å | |||||||||
Authors | Nam, K.H. | |||||||||
Funding support | Korea, Republic Of, 2items
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Citation | Journal: J.Inorg.Biochem. / Year: 2021 Title: Structural analysis of metal chelation of the metalloproteinase thermolysin by 1,10-phenanthroline. Authors: Nam, K.H. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6lzo.cif.gz | 85.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6lzo.ent.gz | 62.9 KB | Display | PDB format |
PDBx/mmJSON format | 6lzo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6lzo_validation.pdf.gz | 2.1 MB | Display | wwPDB validaton report |
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Full document | 6lzo_full_validation.pdf.gz | 2.1 MB | Display | |
Data in XML | 6lzo_validation.xml.gz | 16.3 KB | Display | |
Data in CIF | 6lzo_validation.cif.gz | 24.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lz/6lzo ftp://data.pdbj.org/pub/pdb/validation_reports/lz/6lzo | HTTPS FTP |
-Related structure data
Related structure data | 6lznC 6ig7S 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 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 | #3: Chemical | ChemComp-PHN / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.3 % |
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Crystal grow | Temperature: 294.15 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: Tris-HCl, glycerol, Ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9795 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: May 27, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→20 Å / Num. obs: 30705 / % possible obs: 99 % / Redundancy: 10.6 % / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.024 / Rrim(I) all: 0.09 / Net I/σ(I): 34.5 |
Reflection shell | Resolution: 1.8→1.83 Å / Rmerge(I) obs: 0.377 / Mean I/σ(I) obs: 4.233 / Num. unique obs: 1490 / Rpim(I) all: 0.142 / Rrim(I) all: 0.405 / % possible all: 98.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6IG7 Resolution: 1.8→19.85 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.875 / SU ML: 0.087 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.128 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 85 Å2 / Biso mean: 28.41 Å2 / Biso min: 15.31 Å2
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Refinement step | Cycle: final / Resolution: 1.8→19.85 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.801→1.848 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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