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Yorodumi- PDB-3gdb: Crystal structure of Spr0440 glycoside hydrolase domain, Endo-D f... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3gdb | ||||||
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Title | Crystal structure of Spr0440 glycoside hydrolase domain, Endo-D from Streptococcus pneumoniae R6 | ||||||
Components | Putative uncharacterized protein spr0440 | ||||||
Keywords | HYDROLASE / alpha-beta-barrels / Cell wall / Peptidoglycan-anchor / Secreted | ||||||
Function / homology | Function and homology information mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase / mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase activity / cell wall / metabolic process / extracellular region / membrane / cytosol Similarity search - Function | ||||||
Biological species | Streptococcus pneumoniae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.87 Å | ||||||
Authors | Jiang, Y.-L. / Frolet, C. / Di-guilmi, A.-M. / Zhou, C.-Z. / Vernet, T. / Chen, Y.-X. | ||||||
Citation | Journal: To be published Title: Crystal structure of Spr0440 glycoside hydrolase domain, Endo-D from Streptococcus pneumoniae R6 Authors: Jiang, Y.-L. / Frolet, C. / Di-guilmi, A.-M. / Zhou, C.-Z. / Vernet, T. / Chen, Y.-X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3gdb.cif.gz | 162.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3gdb.ent.gz | 120.7 KB | Display | PDB format |
PDBx/mmJSON format | 3gdb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gd/3gdb ftp://data.pdbj.org/pub/pdb/validation_reports/gd/3gdb | 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 on special symmetry positions |
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Details | THE PROTEIN IS A MONOMER IN THE SOLUTION.ANALYSIS OF PROTEIN INTERFACES HAS NOT REVEALED ANY SPECIFIC INTERACTIONS THAT COULD RESULT IN THE FORMATION OF STABLE QUATERNARY STRUCTURES. MOST PROBABLY, STRUCTURES DO NOT COMPLEXATE IN SOLUTION. |
-Components
#1: Protein | Mass: 104214.617 Da / Num. of mol.: 1 / Fragment: Glycoside Hydrolase domain, residues 38-953 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: R6 / Gene: spr0440 / Plasmid: pLIM / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta References: UniProt: Q8CZ52, mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase | ||||
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#2: Chemical | #3: Chemical | ChemComp-PGE / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 1.704281 Å3/Da / Density % sol: 27.828815 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 20% w/v Polyethylene glycol 4000, 0.1M Sodium acetate trihydrate pH 4.6, 10% Glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 1.86→24.66 Å / Num. obs: 57291 / % possible obs: 97.1 % / Redundancy: 3.4 % / Biso Wilson estimate: 20.9 Å2 / Rmerge(I) obs: 0.066 / Rsym value: 0.078 / Net I/σ(I): 14.7 / Num. measured all: 197385 | ||||||||||||||||||
Reflection shell | Resolution: 1.86→1.98 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.406 / Mean I/σ(I) obs: 3.1 / Num. unique all: 7581 / Rsym value: 0.482 / % possible all: 88.4 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.87→24.66 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.945 / SU B: 3.155 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.133 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.169 Å2
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Refinement step | Cycle: LAST / Resolution: 1.87→24.66 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.866→1.915 Å / Total num. of bins used: 20
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