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Yorodumi- PDB-4rn7: The crystal structure of N-acetylmuramoyl-L-alanine amidase from ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4rn7 | ||||||
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Title | The crystal structure of N-acetylmuramoyl-L-alanine amidase from Clostridium difficile 630 | ||||||
Components | N-acetylmuramoyl-L-alanine amidase | ||||||
Keywords | HYDROLASE / structural genomics / Center for Structural Genomics of Infectious Diseases / CSGID | ||||||
Function / homology | Function and homology information N-acetylmuramoyl-L-alanine amidase / N-acetylmuramoyl-L-alanine amidase activity / peptidoglycan catabolic process / membrane => GO:0016020 / metal ion binding Similarity search - Function | ||||||
Biological species | Peptoclostridium difficile (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.717 Å | ||||||
Authors | Tan, K. / Mulligan, R. / Kwon, K. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Citation | Journal: To be Published Title: The crystal structure of N-acetylmuramoyl-L-alanine amidase from Clostridium difficile 630 Authors: Tan, K. / Mulligan, R. / Kwon, K. / Anderson, W.F. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4rn7.cif.gz | 88.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4rn7.ent.gz | 71.4 KB | Display | PDB format |
PDBx/mmJSON format | 4rn7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rn/4rn7 ftp://data.pdbj.org/pub/pdb/validation_reports/rn/4rn7 | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 20886.156 Da / Num. of mol.: 1 / Fragment: UNP residues 117-301 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Peptoclostridium difficile (bacteria) / Strain: 630 / Gene: CD630_27610 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic References: UniProt: Q183J9, N-acetylmuramoyl-L-alanine amidase |
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-Non-polymers , 5 types, 129 molecules
#2: Chemical | ChemComp-ZN / | ||||
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#3: Chemical | ChemComp-GOL / | ||||
#4: Chemical | #5: Chemical | #6: 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: 2.93 Å3/Da / Density % sol: 58.04 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1M HEPES, 25% w/v PEG3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97899 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 18, 2013 / Details: mirror |
Radiation | Monochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97899 Å / Relative weight: 1 |
Reflection | Resolution: 1.72→28.8 Å / Num. all: 26769 / Num. obs: 26769 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -5 / Redundancy: 8.3 % / Biso Wilson estimate: 27.45 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 54.7 |
Reflection shell | Resolution: 1.72→1.75 Å / Redundancy: 8.4 % / Rmerge(I) obs: 0.717 / Mean I/σ(I) obs: 3.3 / Num. unique all: 1344 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.717→28.755 Å / SU ML: 0.17 / σ(F): 1.34 / Phase error: 23.97 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.717→28.755 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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