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Yorodumi- PDB-4x36: Crystal structure of the autolysin LytA from Streptococcus pneumo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4x36 | |||||||||||||||
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Title | Crystal structure of the autolysin LytA from Streptococcus pneumoniae TIGR4 | |||||||||||||||
Components | Autolysin | |||||||||||||||
Keywords | HYDROLASE / Autolysin / amidase | |||||||||||||||
Function / homology | Function and homology information N-acetylmuramoyl-L-alanine amidase / establishment of competence for transformation / N-acetylmuramoyl-L-alanine amidase activity / sporulation resulting in formation of a cellular spore / peptidoglycan catabolic process / cell wall organization / extracellular region Similarity search - Function | |||||||||||||||
Biological species | Streptococcus pneumoniae TIGR4 (bacteria) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.101 Å | |||||||||||||||
Authors | Cheng, W. / Li, Q. / Zhou, C.Z. / Chen, Y.X. | |||||||||||||||
Funding support | China, 4items
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Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2015 Title: Full-length structure of the major autolysin LytA. Authors: Li, Q. / Cheng, W. / Morlot, C. / Bai, X.H. / Jiang, Y.L. / Wang, W. / Roper, D.I. / Vernet, T. / Dong, Y.H. / Chen, Y. / Zhou, C.Z. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4x36.cif.gz | 82.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4x36.ent.gz | 65 KB | Display | PDB format |
PDBx/mmJSON format | 4x36.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x3/4x36 ftp://data.pdbj.org/pub/pdb/validation_reports/x3/4x36 | 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: 36914.523 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pneumoniae TIGR4 (bacteria) Gene: lytA, SP_1937 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 References: UniProt: P06653, N-acetylmuramoyl-L-alanine amidase | ||||||
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#2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-ZN / | #4: Chemical | ChemComp-CHT / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 4.19 Å3/Da / Density % sol: 70.65 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.1 M Bis-tris propane pH 7.0, 1.3 M ammonium tartrate dibasic |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 19, 2012 |
Radiation | Monochromator: Si(lll) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 36872 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 9.3 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 17 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 9.4 % / Rmerge(I) obs: 0.469 / Mean I/σ(I) obs: 4.9 / % possible all: 100 |
-Processing
Software |
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Refinement | Resolution: 2.101→46.632 Å / SU ML: 0.61 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.04 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.531 Å2 / ksol: 0.363 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.101→46.632 Å
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Refine LS restraints |
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LS refinement shell |
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