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Yorodumi- PDB-4bqo: Structural insights into WcbI, a novel polysaccharide biosynthesi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4bqo | ||||||
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Title | Structural insights into WcbI, a novel polysaccharide biosynthesis enzyme. Native protein without disulfide bond between COA and Cys14. | ||||||
Components | PUTATIVE CAPSULAR POLYSACCHARIDE BIOSYNTHESIS PROTEIN | ||||||
Keywords | TRANSFERASE / ACETYLTRANSFERASE / MELIOIDOSIS | ||||||
Function / homology | Function and homology information Arc Repressor Mutant, subunit A - #2490 / Rossmann fold - #12080 / Polysaccharide biosynthesis enzyme WcbI / Polysaccharide biosynthesis enzyme WcbI / Arc Repressor Mutant, subunit A / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | BURKHOLDERIA PSEUDOMALLEI (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.56 Å | ||||||
Authors | Vivoli, M. / Ayres, E. / Isupov, M.N. / Harmer, N.J. | ||||||
Citation | Journal: Iucrj / Year: 2014 Title: Structural Insights Into Wcbi, a Novel Polysaccharide-Biosynthesis Enzyme. Authors: Vivoli, M. / Ayres, E. / Beaumont, E. / Isupov, M.N. / Harmer, N.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4bqo.cif.gz | 167.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4bqo.ent.gz | 134.9 KB | Display | PDB format |
PDBx/mmJSON format | 4bqo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4bqo_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 4bqo_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 4bqo_validation.xml.gz | 37 KB | Display | |
Data in CIF | 4bqo_validation.cif.gz | 54.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bq/4bqo ftp://data.pdbj.org/pub/pdb/validation_reports/bq/4bqo | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.99496, 0.02571, 0.09694), Vector: |
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 36098.941 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) BURKHOLDERIA PSEUDOMALLEI (bacteria) / Strain: K96243 / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA / References: UniProt: Q63R74 |
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-Non-polymers , 5 types, 740 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-PGE / | #5: Chemical | ChemComp-BR / #6: 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: 2.63 Å3/Da / Density % sol: 53 % / Description: NONE |
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Crystal grow | pH: 7 Details: 10% (W/V) PEG 8000, 75 MM LICL, 75 MM MGCL2, 0.05 M HEPES PH 7.0-8.0. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Oct 23, 2010 |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.56→63.7 Å / Num. obs: 92966 / % possible obs: 92 % / Redundancy: 3.9 % / Biso Wilson estimate: 31.6 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 13 |
Reflection shell | Resolution: 1.56→1.6 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 2.2 / % possible all: 72.6 |
-Processing
Software |
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Refinement | Method to determine structure: MAD Starting model: NONE Resolution: 1.56→44 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.954 / SU B: 1.634 / SU ML: 0.059 / Cross valid method: THROUGHOUT / ESU R: 0.089 / ESU R Free: 0.091 / 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: 28.464 Å2
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Refinement step | Cycle: LAST / Resolution: 1.56→44 Å
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Refine LS restraints |
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