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Open data
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Basic information
Entry | Database: PDB / ID: 3hda | ||||||
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Title | PrtC methionine mutants: M226A_DESY | ||||||
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![]() | HYDROLASE / Met-turn / beta roll / metalloprotease / metzincin / Metal-binding / Protease / Secreted / Zymogen | ||||||
Function / homology | ![]() serralysin / collagen catabolic process / extracellular matrix organization / extracellular matrix / metalloendopeptidase activity / calcium ion binding / proteolysis / extracellular space / zinc ion binding Similarity search - Function | ||||||
Biological species | ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Oberholzer, A.E. / Bumann, M. / Hege, T. / Russo, S. / Baumann, U. | ||||||
![]() | ![]() 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. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 168 KB | Display | ![]() |
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PDB format | ![]() | 130.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 433.8 KB | Display | ![]() |
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Full document | ![]() | 435.2 KB | Display | |
Data in XML | ![]() | 17.5 KB | Display | |
Data in CIF | ![]() | 25.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3hb2C ![]() 3hbuC ![]() 3hbvC ![]() 1go8S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() 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: ![]() |
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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: ![]() ![]() ![]() |
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: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() 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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