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Open data
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Basic information
Entry | Database: PDB / ID: 3hbv | ||||||
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Title | PrtC methionine mutants: M226A in-house | ||||||
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![]() | HYDROLASE / Met-turn / beta roll / zinc / metalloprotease / metzincin / Calcium / 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 | ![]() unidentified (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 | ![]() | 175.6 KB | Display | ![]() |
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PDB format | ![]() | 135.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 436.7 KB | Display | ![]() |
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Full document | ![]() | 437.6 KB | Display | |
Data in XML | ![]() | 21.4 KB | Display | |
Data in CIF | ![]() | 34.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3hb2C ![]() 3hbuC ![]() 3hdaC ![]() 1go8S S: Starting model for refinement C: citing same article ( |
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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
-Protein / Protein/peptide , 2 types, 2 molecules PZ
#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: 646.713 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) unidentified (others) |
-Non-polymers , 4 types, 585 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-CA / #4: Chemical | #5: Chemical | ChemComp-CL / #6: Water | ChemComp-HOH / | |
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-Details
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. |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.66 Å3/Da / Density % sol: 66.41 % |
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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: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 20, 2003 / Details: Si[111], mirrors |
Radiation | Monochromator: RIGAKU OSMIC MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.812 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→50 Å / Num. obs: 54277 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 6 % / Rmerge(I) obs: 0.034 / Net I/σ(I): 3.773 |
Reflection shell | Resolution: 1.95→1.99 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.184 / Mean I/σ(I) obs: 7.5 / Num. unique all: 2670 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1GO8 Resolution: 1.95→29.346 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.915 / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ML / Details: 14.55
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 64.843 Å2 / ksol: 0.392 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 87.58 Å2 / Biso mean: 27.888 Å2 / Biso min: 12.75 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→29.346 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: 12
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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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