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- PDB-1m21: Crystal structure analysis of the peptide amidase PAM in complex ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1m21 | |||||||||
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Title | Crystal structure analysis of the peptide amidase PAM in complex with the competitive inhibitor chymostatin | |||||||||
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![]() | HYDROLASE/HYDROLASE INHIBITOR / Protein-Inhibitor Complex / core: eleven-stranded beta-sheet / covered: double layers of alpha helices on top and bottom / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR COMPLEX | |||||||||
Function / homology | ![]() Amidase signature (AS) enzymes / Amidase signature (AS) domain / Amidase signature domain / Amidase signature (AS) superfamily / Amidase / Prokaryotic membrane lipoprotein lipid attachment site profile. / Alpha-Beta Complex / Alpha Beta Similarity search - Domain/homology | |||||||||
Biological species | ![]() ![]() MC521-C8 | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Labahn, J. / Neumann, S. / Buldt, G. / Kula, M.-R. / Granzin, J. | |||||||||
![]() | ![]() Title: An alternative mechanism for amidase signature enzymes Authors: Labahn, J. / Neumann, S. / Buldt, G. / Kula, M.-R. / Granzin, J. #1: ![]() Title: Crystallization and preliminary X-ray data of the recombinant peptide amidase from Stenotrophomonas maltophilia Authors: Neumann, S. / Granzin, J. / Kula, M.-R. / Labahn, J. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 201.7 KB | Display | ![]() |
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PDB format | ![]() | 158.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 451.4 KB | Display | ![]() |
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Full document | ![]() | 460.1 KB | Display | |
Data in XML | ![]() | 39.2 KB | Display | |
Data in CIF | ![]() | 57 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1m22SC 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Details | two biological entities are in the asym. unit |
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Components
#1: Protein | Mass: 53545.301 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Plasmid: pEK06 / Production host: ![]() ![]() References: UniProt: Q8RJN5, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides #2: Protein/peptide | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.83 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: PEG6000, HEPES, Glycerine, Sodium Azide, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Details: Neumann, S., (2002) Acta Crystallogr., Sect.D, 58, 333. | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jul 12, 2001 |
Radiation | Monochromator: Diamond(111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→60.29 Å / Num. all: 87122 / Num. obs: 87122 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 11.9 Å2 / Rmerge(I) obs: 0.099 / Rsym value: 0.085 / Net I/σ(I): 6.1 |
Reflection shell | Resolution: 1.8→1.91 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.273 / Mean I/σ(I) obs: 3 / Rsym value: 0.207 / % possible all: 79.9 |
Reflection | *PLUS Highest resolution: 1.78 Å / Num. obs: 89189 / % possible obs: 98.1 % / Rmerge(I) obs: 0.099 |
Reflection shell | *PLUS % possible obs: 79.9 % / Rmerge(I) obs: 0.273 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1M22 Resolution: 1.8→60.29 Å / Rfactor Rfree error: 0.003 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 36.5977 Å2 / ksol: 0.386826 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→60.29 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 100 Å / % reflection Rfree: 5 % / Rfactor obs: 0.203 / Rfactor Rfree: 0.216 / Rfactor Rwork: 0.203 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.247 / Rfactor Rwork: 0.226 |