+Open data
-Basic information
Entry | Database: PDB / ID: 3hda | ||||||
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Title | PrtC methionine mutants: M226A_DESY | ||||||
Components |
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Keywords | HYDROLASE / Met-turn / beta roll / metalloprotease / metzincin / Metal-binding / Protease / Secreted / Zymogen | ||||||
Function / homology | Function and homology information serralysin / extracellular matrix / metalloendopeptidase activity / calcium ion binding / proteolysis / extracellular space / zinc ion binding Similarity search - Function | ||||||
Biological species | Erwinia chrysanthemi (bacteria) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.131 Å | ||||||
Authors | Oberholzer, A.E. / Bumann, M. / Hege, T. / Russo, S. / Baumann, U. | ||||||
Citation | Journal: Biol.Chem. / Year: 2009 Title: Metzincin's canonical methionine is responsible for the structural integrity of the zinc-binding site Authors: Oberholzer, A.E. / Bumann, M. / Hege, T. / Russo, S. / Baumann, U. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3hda.cif.gz | 168 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3hda.ent.gz | 130.3 KB | Display | PDB format |
PDBx/mmJSON format | 3hda.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hd/3hda ftp://data.pdbj.org/pub/pdb/validation_reports/hd/3hda | HTTPS FTP |
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-Related structure data
Related structure data | 3hb2C 3hbuC 3hbvC 1go8S 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: 49706.043 Da / Num. of mol.: 1 / Mutation: M226A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Erwinia chrysanthemi (bacteria) / Gene: prtC / Plasmid: pUC18 derivative / Production host: Escherichia coli (E. coli) / Strain (production host): XL1BLUE References: UniProt: P16317, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases | ||||||
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#2: Protein/peptide | Mass: 559.569 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) | ||||||
#3: Chemical | ChemComp-CA / #4: Chemical | #5: Water | ChemComp-HOH / | Sequence details | THE AUTHOR STATES THAT THE ORIGIN OF THE PEPTIDE IS UNCLEAR. THE SEQUENCE IS BASED ON THE SHAPE OF ...THE AUTHOR STATES THAT THE ORIGIN OF THE PEPTIDE IS UNCLEAR. THE SEQUENCE IS BASED ON THE SHAPE OF THE ELECTRON DENSITY MAP. | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.65 Å3/Da / Density % sol: 66.26 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 2 M NaCl, 0.1 M phosphate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.812 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Oct 1, 2003 / Details: Mirrors |
Radiation | Monochromator: Si[111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.812 Å / Relative weight: 1 |
Reflection | Resolution: 2.13→50 Å / Num. all: 41603 / Num. obs: 41603 / % possible obs: 99.9 % / Observed criterion σ(F): -6 / Observed criterion σ(I): -3 / Redundancy: 6.7 % / Rmerge(I) obs: 0.083 / Χ2: 0.968 / Net I/σ(I): 19.709 |
Reflection shell | Resolution: 2.13→2.17 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.396 / Num. unique all: 2043 / Χ2: 0.959 / % possible all: 100 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1GO8 Resolution: 2.131→26.508 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.867 / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / σ(I): 0 / Phase error: 19.98 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.016 Å2 / ksol: 0.402 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 105.85 Å2 / Biso mean: 35.693 Å2 / Biso min: 13.52 Å2
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Refinement step | Cycle: LAST / Resolution: 2.131→26.508 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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