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Open data
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Basic information
Entry | Database: PDB / ID: 1u10 | ||||||
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Title | MEPA, active form with ZN in P1 | ||||||
![]() | 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. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 286.3 KB | Display | ![]() |
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PDB format | ![]() | 233.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 493.3 KB | Display | ![]() |
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Full document | ![]() | 518.4 KB | Display | |
Data in XML | ![]() | 51.7 KB | Display | |
Data in CIF | ![]() | 69.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1tzpSC 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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3 | ![]()
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Unit cell |
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Details | Dimer in three different crystal forms. Oligomeric state in solution not characterized. |
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Components
#1: Protein | Mass: 28612.814 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P14007, UniProt: P0C0T5*PLUS, EC: 3.4.99.- #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40.22 % Description: The number of reflections reported here include anomalous data. |
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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, 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 27, 2004 | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.4→20 Å / Num. all: 103423 / Num. obs: 103423 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.9 % / Biso Wilson estimate: 36 Å2 / Rmerge(I) obs: 0.039 / Rsym value: 0.039 / Net I/σ(I): 14.1 | ||||||||||||
Reflection shell | Resolution: 2.4→2.44 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.151 / Mean I/σ(I) obs: 4 / Num. unique all: 4917 / Rsym value: 0.151 / % possible all: 93.5 |
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Processing
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Refinement | Method to determine structure: MAD combined with molecular replacement Starting model: MepA in the P21 form (1TZP) Resolution: 2.4→20 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.888 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.918 / ESU R Free: 0.312 / 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: 24.954 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→20 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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