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Yorodumi- PDB-3ban: The crystal structure of mannonate dehydratase from Streptococcus... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ban | ||||||
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Title | The crystal structure of mannonate dehydratase from Streptococcus suis serotype2 | ||||||
Components | D-mannonate dehydratase | ||||||
Keywords | LYASE / xylose-like TIM barrel | ||||||
Function / homology | Function and homology information D-glucuronate catabolic process / mannonate dehydratase / mannonate dehydratase activity / ferrous iron binding / manganese ion binding Similarity search - Function | ||||||
Biological species | Streptococcus suis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Peng, H. / Zhang, Q.M. / Gao, F. / Liu, Y.W. / Qi, J.X. / Gao, G.F. | ||||||
Citation | Journal: To be Published Title: The crystal structure of mannonate dehydratase from Streptococcus suis serotype2 Authors: Peng, H. / Zhang, Q.M. / Gao, F. / Liu, Y.W. / Qi, J.X. / Gao, G.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ban.cif.gz | 144.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ban.ent.gz | 114.5 KB | Display | PDB format |
PDBx/mmJSON format | 3ban.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ban_validation.pdf.gz | 445.5 KB | Display | wwPDB validaton report |
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Full document | 3ban_full_validation.pdf.gz | 467.3 KB | Display | |
Data in XML | 3ban_validation.xml.gz | 26.9 KB | Display | |
Data in CIF | 3ban_validation.cif.gz | 36.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ba/3ban ftp://data.pdbj.org/pub/pdb/validation_reports/ba/3ban | HTTPS FTP |
-Related structure data
Related structure data | 1tz9S S: Starting model for refinement |
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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: 43024.559 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus suis (bacteria) / Strain: Serotype 2, strain 05ZYH33 / Gene: UxuA / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / References: UniProt: A4VVI4, mannonate dehydratase |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.59 Å3/Da / Density % sol: 52.5 % |
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-Data collection
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 |
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Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.9→105.409 Å / Num. obs: 20728 / Redundancy: 13.85 % / Biso Wilson estimate: 61.2 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 2.9→3 Å / Redundancy: 14.13 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 5.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1TZ9 Resolution: 2.9→44.06 Å / Cor.coef. Fo:Fc: 0.888 / Cor.coef. Fo:Fc free: 0.854 / SU B: 18.594 / SU ML: 0.361 / Cross valid method: THROUGHOUT / ESU R Free: 0.446 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.716 Å2
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Refinement step | Cycle: LAST / Resolution: 2.9→44.06 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→2.975 Å / Total num. of bins used: 20
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