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- PDB-1m22: X-ray structure of native peptide amidase from Stenotrophomonas m... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1m22 | ||||||
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Title | X-ray structure of native peptide amidase from Stenotrophomonas maltophilia at 1.4 A | ||||||
![]() | peptide amidase | ||||||
![]() | HYDROLASE / eleven-stranded beta sheet / covered double layers of alpha helices on top and bottom | ||||||
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 / Peptide amidase![]() | ||||||
Biological species | ![]() | ||||||
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. #2: ![]() Title: Purification and characterisation of a newly screened microbial peptide amidase Authors: Stelkes-Ritter, U. / Wyzgol, K. / Kula, M.-R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 218.6 KB | Display | ![]() |
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PDB format | ![]() | 171.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 456.1 KB | Display | ![]() |
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Full document | ![]() | 469.3 KB | Display | |
Data in XML | ![]() | 48.1 KB | Display | |
Data in CIF | ![]() | 73.5 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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2 | ![]()
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Unit cell |
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Details | the biological unit is the monomer |
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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: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.29 % | ||||||||||||||||||||||||||||||||||||
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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, vapour diffusion, sitting drop, temperature 289K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, sitting dropDetails: 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: 1.4→79 Å / Num. all: 182206 / Num. obs: 182206 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 11.9 Å2 / Rmerge(I) obs: 0.103 / Net I/σ(I): 7.8 |
Reflection shell | Resolution: 1.4→1.49 Å / Rmerge(I) obs: 0.169 / Mean I/σ(I) obs: 5.1 / % possible all: 95 |
Reflection | *PLUS Lowest resolution: 79 Å / Rmerge(I) obs: 0.103 |
Reflection shell | *PLUS % possible obs: 95 % / Rmerge(I) obs: 0.169 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 44.5075 Å2 / ksol: 0.380289 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.4→79 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTR | ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.4→1.49 Å / Rfactor Rfree error: 0.007 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 1.4 Å / Lowest resolution: 100 Å / Rfactor all: 0.18 / Rfactor obs: 0.189 / Rfactor Rfree: 0.199 / Rfactor Rwork: 0.188 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.26 / Rfactor Rwork: 0.25 |