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Yorodumi- PDB-2ae0: Crystal structure of MltA from Escherichia coli reveals a unique ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ae0 | ||||||
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Title | Crystal structure of MltA from Escherichia coli reveals a unique lytic transglycosylase fold | ||||||
Components | Membrane-bound lytic murein transglycosylase A | ||||||
Keywords | HYDROLASE / double-psi beta-barrel / small mixed parallel/antiparallel six stranded beta barrel / helical sub-domain | ||||||
Function / homology | Function and homology information : / lytic transglycosylase activity / peptidoglycan turnover / hydrolase activity, hydrolyzing O-glycosyl compounds / peptidoglycan catabolic process / cell wall organization / cell outer membrane / outer membrane-bounded periplasmic space Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å | ||||||
Authors | Van Straaten, K.E. / Dijkstra, B.W. / Vollmer, W. / Thunnissen, A.M.W.H. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2005 Title: Crystal Structure of MltA from Escherichia coli Reveals a Unique Lytic Transglycosylase Fold Authors: van Straaten, K.E. / Dijkstra, B.W. / Vollmer, W. / Thunnissen, A.M.W.H. | ||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR DETERMINED |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ae0.cif.gz | 84.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ae0.ent.gz | 63.1 KB | Display | PDB format |
PDBx/mmJSON format | 2ae0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ae/2ae0 ftp://data.pdbj.org/pub/pdb/validation_reports/ae/2ae0 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 38250.688 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: mlta / Production host: Escherichia coli (E. coli) References: UniProt: P0A935, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds |
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#2: Chemical | ChemComp-EDO / |
#3: Chemical | ChemComp-ACY / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.47 Å3/Da / Density % sol: 72.47 % |
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Crystal grow | Temperature: 280 K / Method: vapor diffusion, hanging drop / pH: 4.2 Details: PEG 8000, sodium chloride, sodium acetate, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 280K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934, 0.9794, 0.9792, 0.9393 | |||||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 23, 2002 | |||||||||||||||
Radiation | Monochromator: diamonds (111), Ge(220) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2→30 Å / Num. all: 46854 / Num. obs: 46854 / % possible obs: 100 % / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.049 / Χ2: 0.934 | |||||||||||||||
Reflection shell | Resolution: 2→2.07 Å / % possible obs: 100 % / Rmerge(I) obs: 0.501 / Num. measured obs: 4652 / Χ2: 0.866 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.932 / SU B: 3.13 / SU ML: 0.086 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.124 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 37.227 Å2
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Refinement step | Cycle: LAST / Resolution: 2→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.02 Å / Total num. of bins used: 50
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Refinement TLS params. | Method: refined / Origin x: 3.796 Å / Origin y: 48.52 Å / Origin z: 52.515 Å
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