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Open data
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Basic information
Entry | Database: PDB / ID: 1tzp | ||||||
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Title | MEPA, inactive form without ZN in P21 | ||||||
![]() | Penicillin-insensitive murein endopeptidase | ||||||
![]() | HYDROLASE / LAS enzyme / metallopeptidase / peptidoglycan hydrolase | ||||||
Function / homology | ![]() peptidoglycan metabolic process / Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / peptidoglycan biosynthetic process / metalloendopeptidase activity / peptidase activity / outer membrane-bounded periplasmic space / endopeptidase activity / response to xenobiotic stimulus / serine-type endopeptidase activity / proteolysis / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Marcyjaniak, M. / Odintsov, S.G. / Sabala, I. / Bochtler, M. | ||||||
![]() | ![]() Title: Peptidoglycan amidase MepA is a LAS metallopeptidase Authors: Marcyjaniak, M. / Odintsov, S.G. / Sabala, I. / Bochtler, M. #1: Journal: Protein Sci. / Year: 2004 Title: Similar active sites in lysostaphins and D-Ala-D-Ala metallopeptidases Authors: Bochtler, M. / Odintsov, S.G. / Marcyjaniak, M. / Sabala, I. #2: ![]() Title: Latent LytM at 1.3A resolution Authors: Odintsov, S.G. / Sabala, I. / Marcyjaniak, M. / Bochtler, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 119 KB | Display | ![]() |
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PDB format | ![]() | 91.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Details | Dimer in three different crystal forms.lution not characterized |
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Components
#1: Protein | Mass: 28331.443 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P14007, UniProt: P0C0T5*PLUS, EC: 3.4.99.- #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-BU1 / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 45.9 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: ammonium sulfate, MES, PEG monomethyl ether 5000, 1,4-butanediol, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Apr 26, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.05 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→20 Å / Num. obs: 91010 / % possible obs: 91.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 14.2 Å2 / Rmerge(I) obs: 0.036 / Rsym value: 0.036 / Net I/σ(I): 10 |
Reflection shell | Resolution: 1.4→1.48 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.129 / Mean I/σ(I) obs: 5.5 / Num. unique all: 13722 / Rsym value: 0.129 / % possible all: 94.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: A partial model of MEPA in a different crystal form Resolution: 1.4→19.73 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.949 / SU B: 0.957 / SU ML: 0.039 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.067 / ESU R Free: 0.068 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 13.402 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→19.73 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.4→1.436 Å / Total num. of bins used: 20 /
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