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- PDB-3ami: The crystal structure of the M16B metallopeptidase subunit from S... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3ami | ||||||
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Title | The crystal structure of the M16B metallopeptidase subunit from Sphingomonas sp. A1 | ||||||
![]() | zinc peptidase | ||||||
![]() | HYDROLASE / alpha/beta / peptidase / zinc binding | ||||||
Function / homology | ![]() Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Maruyama, Y. / Chuma, A. / Mikami, B. / Hashimoto, W. / Murata, K. | ||||||
![]() | ![]() Title: Heterosubunit composition and crystal structures of a novel bacterial M16B metallopeptidase Authors: Maruyama, Y. / Chuma, A. / Mikami, B. / Hashimoto, W. / Murata, K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 174 KB | Display | ![]() |
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PDB format | ![]() | 138.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 433.5 KB | Display | ![]() |
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Full document | ![]() | 450.2 KB | Display | |
Data in XML | ![]() | 32.9 KB | Display | |
Data in CIF | ![]() | 45.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Details | AUTHOR DEFINED BIOLOGICAL UNIT: UNKNOWN. HOWEVER, AUTHOR CONFIRMED THE MOLECULAR TO BE MONOMER IN VITRO USING GEL FILTRATION COLUMN CHROMATOGRAPHY. |
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Components
#1: Protein | Mass: 49470.754 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: F2Z284*PLUS, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases #2: Water | ChemComp-HOH / | Sequence details | THE SEQUENCE OF THE PROTEIN HAS BEEN DEPOSITED TO DDBJ, BUT IS NOT PUBLICLY AVAILABLE AT THE TIME ...THE SEQUENCE OF THE PROTEIN HAS BEEN DEPOSITED TO DDBJ, BUT IS NOT PUBLICLY AVAILABLE AT THE TIME OF PROCESSING | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 43.01 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: 12% PEG 4000, 0.1M litium sulfate, 0.1M sodium citrate, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. obs: 32754 / % possible obs: 100 % / Rmerge(I) obs: 0.133 / Net I/σ(I): 18.33 |
Reflection shell | Resolution: 2.4→2.49 Å / Rmerge(I) obs: 0.356 / Mean I/σ(I) obs: 4.47 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.949 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→42.78 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.462 Å / Total num. of bins used: 20
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