+Open data
-Basic information
Entry | Database: PDB / ID: 6yze | ||||||
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Title | Zinc metalloprotease ProA from native source | ||||||
Components | Zinc metalloproteinase | ||||||
Keywords | HYDROLASE / ProA / M4 protease / TLP-like / Metalloprotease / zinc / METAL BINDING PROTEIN | ||||||
Function / homology | Function and homology information Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / metalloendopeptidase activity / proteolysis / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | Legionella pneumophila (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.18 Å | ||||||
Authors | Schmelz, S. / Blankenfeldt, W. | ||||||
Citation | Journal: Cell.Microbiol. / Year: 2021 Title: Zinc metalloprotease ProA of Legionella pneumophila increases alveolar septal thickness in human lung tissue explants by collagen IV degradation. Authors: Scheithauer, L. / Thiem, S. / Schmelz, S. / Dellmann, A. / Bussow, K. / Brouwer, R.M.H.J. / Unal, C.M. / Blankenfeldt, W. / Steinert, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6yze.cif.gz | 81.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6yze.ent.gz | 58.9 KB | Display | PDB format |
PDBx/mmJSON format | 6yze.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6yze_validation.pdf.gz | 743.1 KB | Display | wwPDB validaton report |
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Full document | 6yze_full_validation.pdf.gz | 744.9 KB | Display | |
Data in XML | 6yze_validation.xml.gz | 14.5 KB | Display | |
Data in CIF | 6yze_validation.cif.gz | 20.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yz/6yze ftp://data.pdbj.org/pub/pdb/validation_reports/yz/6yze | HTTPS FTP |
-Related structure data
Related structure data | 6ya1C 3nqxS 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
#1: Protein | Mass: 37788.734 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Legionella pneumophila (bacteria) References: UniProt: P21347, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases |
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#2: Chemical | ChemComp-ZN / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
Has protein modification | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.98 Å3/Da / Density % sol: 38 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: 16 mg/ml native ProA 1 M sodium acetate pH 4.5 and 1.2 M tri-sodium citrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5419 Å | ||||||||||||||||||||||||||||||
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Oct 18, 2017 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5419 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.18→50.59 Å / Num. obs: 16137 / % possible obs: 98.5 % / Redundancy: 5.1 % / CC1/2: 0.993 / Rmerge(I) obs: 0.138 / Rpim(I) all: 0.066 / Rrim(I) all: 0.153 / Net I/σ(I): 9.7 / Num. measured all: 82983 / Scaling rejects: 6 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3nqx Resolution: 2.18→38.9 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.73
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 71.31 Å2 / Biso mean: 25.0782 Å2 / Biso min: 8.36 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.18→38.9 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6
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