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Yorodumi- PDB-5k8b: X-ray structure of KdnA, 8-amino-3,8-dideoxy-alpha-D-manno-octulo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5k8b | ||||||
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Title | X-ray structure of KdnA, 8-amino-3,8-dideoxy-alpha-D-manno-octulosonate transaminase, from Shewanella oneidensis in the presence of the external aldimine with PLP and glutamate | ||||||
Components | 8-amino-3,8-dideoxy-alpha-D-manno-octulosonate transaminase | ||||||
Keywords | TRANSFERASE / Transaminase / 8-amino-3 / 8-dideoxy-d-manno-octulosonic acid / deoxy sugar | ||||||
Function / homology | Function and homology information 8-amino-3,8-dideoxy-alpha-D-manno-octulosonate transaminase / polysaccharide biosynthetic process / lipopolysaccharide biosynthetic process / transaminase activity / catalytic activity / pyridoxal phosphate binding Similarity search - Function | ||||||
Biological species | Shewanella oneidensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | ||||||
Authors | Holden, H.M. / Thoden, J.B. / Zachman-Brockmeyer, T.R. | ||||||
Funding support | United States, 1items
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Citation | Journal: Biochemistry / Year: 2016 Title: Structures of KdnB and KdnA from Shewanella oneidensis: Key Enzymes in the Formation of 8-Amino-3,8-Dideoxy-d-Manno-Octulosonic Acid. Authors: Zachman-Brockmeyer, T.R. / Thoden, J.B. / Holden, H.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5k8b.cif.gz | 325.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5k8b.ent.gz | 263.7 KB | Display | PDB format |
PDBx/mmJSON format | 5k8b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k8/5k8b ftp://data.pdbj.org/pub/pdb/validation_reports/k8/5k8b | HTTPS FTP |
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-Related structure data
Related structure data | 5k8cC 3frkS C: citing same article (ref.) S: Starting model for refinement |
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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: 44768.273 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Shewanella oneidensis (strain MR-1) (bacteria) Strain: MR-1 / Gene: kdnA, SO_2476 / Production host: Escherichia coli (E. coli) References: UniProt: Q8EEB1, 8-amino-3,8-dideoxy-alpha-D-manno-octulosonate transaminase #2: Chemical | ChemComp-PDG / #3: Chemical | ChemComp-CL / #4: Chemical | ChemComp-NA / | #5: 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: 2.24 Å3/Da / Density % sol: 45.02 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 16-21% PEG-3350, 100 mM MES, 200 mM KCl, 150 mM MgCl2, 1 mM PLP, 50 mM monosodium glutamate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: Bruker Platinum 135 / Detector: CCD / Date: Sep 22, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→50 Å / Num. obs: 83041 / % possible obs: 95.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Rmerge(I) obs: 0.078 / Rsym value: 0.078 / Net I/σ(I): 7.8 |
Reflection shell | Resolution: 2.15→2.25 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.254 / Mean I/σ(I) obs: 2.4 / % possible all: 89.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3FRK Resolution: 2.15→50 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.916 / SU B: 6.549 / SU ML: 0.163 / Cross valid method: THROUGHOUT / ESU R: 0.265 / ESU R Free: 0.203 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.988 Å2
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Refinement step | Cycle: 1 / Resolution: 2.15→50 Å
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