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Yorodumi- PDB-3bdk: Crystal Structure of Streptococcus suis mannonate dehydratase com... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3bdk | ||||||
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Title | Crystal Structure of Streptococcus suis mannonate dehydratase complexed with substrate analogue | ||||||
Components | D-mannonate dehydratase | ||||||
Keywords | LYASE / Xylose isomerase-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: 2.5 Å | ||||||
Authors | Gao, F. / Zhang, Q.M. / Peng, H. / Liu, Y.W. / Qi, J.X. / Gao, G.F. | ||||||
Citation | Journal: To be Published Title: Crystal structure of Streptococcus suis mannonate dehydratase complexed with substrate analogue Authors: Gao, F. / Zhang, Q.M. / Peng, H. / 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 | 3bdk.cif.gz | 147.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3bdk.ent.gz | 115.4 KB | Display | PDB format |
PDBx/mmJSON format | 3bdk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3bdk_validation.pdf.gz | 463.6 KB | Display | wwPDB validaton report |
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Full document | 3bdk_full_validation.pdf.gz | 483.5 KB | Display | |
Data in XML | 3bdk_validation.xml.gz | 27.9 KB | Display | |
Data in CIF | 3bdk_validation.cif.gz | 38.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bd/3bdk ftp://data.pdbj.org/pub/pdb/validation_reports/bd/3bdk | HTTPS FTP |
-Related structure data
Related structure data | 1vl8S 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: strain 05ZYH33 / Gene: UxuA / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / References: UniProt: A4VVI4, mannonate dehydratase #2: Sugar | ChemComp-DNO / | #3: Chemical | ChemComp-MN / | #4: Water | ChemComp-HOH / | |
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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: 52.47 % |
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Crystal grow | Method: evaporation / Details: EVAPORATION |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. obs: 31751 / Redundancy: 13.3 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 39.9 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 8.8 % / Rmerge(I) obs: 0.509 / Mean I/σ(I) obs: 2.98 / Num. unique all: 2817 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1vl8 Resolution: 2.5→45.27 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.872 / SU B: 12.216 / SU ML: 0.276 / Cross valid method: THROUGHOUT / ESU R: 0.59 / ESU R Free: 0.344 / 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: 44.905 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→45.27 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.503→2.568 Å / Total num. of bins used: 20
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