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Yorodumi- PDB-2xqx: Structure of the family 32 carbohydrate-binding module from Strep... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2xqx | ||||||
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Title | Structure of the family 32 carbohydrate-binding module from Streptococcus pneumoniae EndoD | ||||||
Components | ENDO-BETA-N-ACETYLGLUCOSAMINIDASE D | ||||||
Keywords | SUGAR BINDING PROTEIN / CARBOHYDRATE BINDING / BETA-SANDWHICH | ||||||
Function / homology | Function and homology information mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase activity / metabolic process / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | STREPTOCOCCUS PNEUMONIAE (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.01 Å | ||||||
Authors | Abbott, D.W. / Boraston, A.B. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2011 Title: Structural Analysis of a Putative Family 32 Carbohydrate-Binding Module from the Streptococcus Pneumoniae Enzyme Endod. Authors: Abbott, D.W. / Boraston, A.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2xqx.cif.gz | 73 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xqx.ent.gz | 59 KB | Display | PDB format |
PDBx/mmJSON format | 2xqx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2xqx_validation.pdf.gz | 445.7 KB | Display | wwPDB validaton report |
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Full document | 2xqx_full_validation.pdf.gz | 450.3 KB | Display | |
Data in XML | 2xqx_validation.xml.gz | 16.9 KB | Display | |
Data in CIF | 2xqx_validation.cif.gz | 24.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xq/2xqx ftp://data.pdbj.org/pub/pdb/validation_reports/xq/2xqx | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 16901.166 Da / Num. of mol.: 2 / Fragment: CBM32, RESIDUES 804-948 Source method: isolated from a genetically manipulated source Source: (gene. exp.) STREPTOCOCCUS PNEUMONIAE (bacteria) / Strain: TIGR4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q93HW0, UniProt: A0A0H2UNT5*PLUS #2: Chemical | #3: Chemical | ChemComp-ACT / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.47 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 113 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9791 |
Detector | Type: MARRESEARCH / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 2→35 Å / Num. obs: 20817 / % possible obs: 98.1 % / Observed criterion σ(I): 2 / Redundancy: 14.6 % / Biso Wilson estimate: 21.2 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 18.5 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 14.3 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 7.2 / % possible all: 97.4 |
-Processing
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Refinement | Method to determine structure: SAD Starting model: NONE Resolution: 2.01→66.67 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.893 / SU B: 4.536 / SU ML: 0.129 / Cross valid method: THROUGHOUT / ESU R: 0.22 / ESU R Free: 0.19 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.448 Å2
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Refinement step | Cycle: LAST / Resolution: 2.01→66.67 Å
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Refine LS restraints |
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