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Yorodumi- PDB-5oq3: High resolution structure of the functional region of Cwp19 from ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5oq3 | ||||||
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Title | High resolution structure of the functional region of Cwp19 from Clostridium difficile | ||||||
Components | Cwp19 | ||||||
Keywords | HYDROLASE / S-layer / glycoside hydrolase / TIM barrel | ||||||
Function / homology | Glycosyl hydrolase-like 10 / Glycosyl hydrolase-like 10 / Putative cell wall binding repeat 2 / Cell wall binding domain 2 (CWB2) / N-acetylmuramoyl-L-alanine amidase activity / Glycoside hydrolase superfamily / DI(HYDROXYETHYL)ETHER / Cwp19 Function and homology information | ||||||
Biological species | Clostridioides difficile (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å | ||||||
Authors | Bradshaw, W.J. / Kirby, J.M. / Roberts, A.K. / Shone, C.C. / Acharya, K.R. | ||||||
Funding support | 1items
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Citation | Journal: FEBS J. / Year: 2017 Title: The molecular structure of the glycoside hydrolase domain of Cwp19 from Clostridium difficile. Authors: Bradshaw, W.J. / Kirby, J.M. / Roberts, A.K. / Shone, C.C. / Acharya, K.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5oq3.cif.gz | 176.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5oq3.ent.gz | 137.1 KB | Display | PDB format |
PDBx/mmJSON format | 5oq3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5oq3_validation.pdf.gz | 436.7 KB | Display | wwPDB validaton report |
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Full document | 5oq3_full_validation.pdf.gz | 437.3 KB | Display | |
Data in XML | 5oq3_validation.xml.gz | 18.3 KB | Display | |
Data in CIF | 5oq3_validation.cif.gz | 28.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oq/5oq3 ftp://data.pdbj.org/pub/pdb/validation_reports/oq/5oq3 | HTTPS FTP |
-Related structure data
Related structure data | 5oq2SC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 44836.090 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridioides difficile (bacteria) Gene: lytC_21, cwp19, lytC_5, SAMEA3374989_00994, SAMEA3375004_02322 Plasmid: pET28a / Production host: Escherichia coli BL21 (bacteria) References: UniProt: L7PGA3, N-acetylmuramoyl-L-alanine amidase |
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#2: Chemical | ChemComp-CL / |
#3: Chemical | ChemComp-EDO / |
#4: Chemical | ChemComp-PEG / |
#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: 2.37 Å3/Da / Density % sol: 48.06 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop Details: 90% (10 mM monobasic potassium phosphate, 18% PEG 8,000) 10% (20 mM D-glucose, 20 mM D-mannose, 20 mM D-galactose, 20 mM L-fucose, 20 mM D-xylose, 20 mM N-acetyl-D-glucosamine |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 1, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→65.64 Å / Num. obs: 93318 / % possible obs: 99.5 % / Redundancy: 25.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.118 / Rpim(I) all: 0.033 / Rrim(I) all: 0.123 / Net I/σ(I): 15.4 |
Reflection shell | Resolution: 1.35→1.37 Å / Redundancy: 23.7 % / Rmerge(I) obs: 0.674 / Mean I/σ(I) obs: 3.7 / Num. unique obs: 4543 / CC1/2: 0.982 / Rpim(I) all: 0.2 / Rrim(I) all: 0.704 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5OQ2 Resolution: 1.35→55.51 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.96 / SU B: 1.971 / SU ML: 0.035 / Cross valid method: THROUGHOUT / ESU R: 0.047 / ESU R Free: 0.045 / 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: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.682 Å2
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Refinement step | Cycle: 1 / Resolution: 1.35→55.51 Å
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Refine LS restraints |
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