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Yorodumi- PDB-1ltm: ACCELERATED X-RAY STRUCTURE ELUCIDATION OF A 36 KDA MURAMIDASE/TR... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ltm | ||||||
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Title | ACCELERATED X-RAY STRUCTURE ELUCIDATION OF A 36 KDA MURAMIDASE/TRANSGLYCOSYLASE USING WARP | ||||||
Components | 36 KDA SOLUBLE LYTIC TRANSGLYCOSYLASE | ||||||
Keywords | GLYCOSYLTRANSFERASE / MURAMIDASE / TRANSGLYCOSYLASE / PEPTIDOGLYCAN MATURATION / LYSOZYME / PERIPLASMIC | ||||||
Function / homology | Function and homology information lytic endotransglycosylase activity / : / lytic transglycosylase activity / sodium ion binding / peptidoglycan catabolic process / cell outer membrane / cell wall organization / outer membrane-bounded periplasmic space / calcium ion binding Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 1.7 Å | ||||||
Authors | Van Asselt, E.J. / Dijkstra, B.W. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 1998 Title: Accelerated X-ray structure elucidation of a 36 kDa muramidase/transglycosylase using wARP. Authors: Van Asselt, E.J. / Perrakis, A. / Kalk, K.H. / Lamzin, V.S. / Dijkstra, B.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ltm.cif.gz | 83.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ltm.ent.gz | 61.1 KB | Display | PDB format |
PDBx/mmJSON format | 1ltm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ltm_validation.pdf.gz | 437.9 KB | Display | wwPDB validaton report |
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Full document | 1ltm_full_validation.pdf.gz | 440.6 KB | Display | |
Data in XML | 1ltm_validation.xml.gz | 16.7 KB | Display | |
Data in CIF | 1ltm_validation.cif.gz | 25.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lt/1ltm ftp://data.pdbj.org/pub/pdb/validation_reports/lt/1ltm | HTTPS FTP |
-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: 35849.336 Da / Num. of mol.: 1 / Fragment: SOLUBLE ACTIVE DOMAIN OF MLTB Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: 122-1 / Cell line: BL21 / Cellular location: PERIPLASM / Gene: MLTB / Plasmid: PAD115 / Species (production host): Escherichia coli / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) References: UniProt: P41052, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds |
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#2: Chemical | ChemComp-NA / |
#3: Chemical | ChemComp-BCN / |
#4: Chemical | ChemComp-EDO / |
#5: 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: 2.72 Å3/Da / Density % sol: 55 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 8.5 Details: ROD-SHAPED CRYSTALS WERE GROWN AT 295 K IN 1 DAY TO 1 WEEK BY EQUILIBRATING A HANGING DROP, THAT CONSISTED OF 3 UL OF PROTEIN SOLUTION AND 3 UL OF RESERVOIR SOLUTION OF 100 MM BICINE-NAOH, ...Details: ROD-SHAPED CRYSTALS WERE GROWN AT 295 K IN 1 DAY TO 1 WEEK BY EQUILIBRATING A HANGING DROP, THAT CONSISTED OF 3 UL OF PROTEIN SOLUTION AND 3 UL OF RESERVOIR SOLUTION OF 100 MM BICINE-NAOH, PH 7.8-8.5 AND 0-6% PEG 20K., vapor diffusion - hanging drop PH range: 7.8-8.5 | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 295 K / pH: 7.2 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.92 |
Detector | Detector: CCD / Date: Apr 8, 1995 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→29.6 Å / Num. obs: 41653 / % possible obs: 94.4 % / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 18.4 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 24.4 |
Reflection shell | Resolution: 1.7→1.73 Å / Rmerge(I) obs: 0.261 / Mean I/σ(I) obs: 3.5 / % possible all: 91.8 |
Reflection | *PLUS Num. measured all: 206582 |
-Processing
Software |
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Refinement | Method to determine structure: MIRAS / Resolution: 1.7→20 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.0001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
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Displacement parameters | Biso mean: 23.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.7→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.81 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.843 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.189 / Rfactor Rwork: 0.187 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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