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Yorodumi- PDB-4k2m: Crystal structure of ntda from bacillus subtilis in complex with ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4k2m | |||||||||
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Title | Crystal structure of ntda from bacillus subtilis in complex with the plp external aldimine adduct with kanosamine-6-phosphate | |||||||||
Components | NTD biosynthesis operon protein NtdA | |||||||||
Keywords | TRANSFERASE / Sugar aminotransferase / Aspertate aminotransferase fold / homo-dimer / additional N-terninal domain / 3-KETO-GLUCOSE-6-PHOSPHATE AMINITRANSFERASE / KANOSAMINE-6-PHOSPHATE | |||||||||
Function / homology | Function and homology information 3-dehydro-glucose-6-phosphate-glutamate transaminase / polysaccharide biosynthetic process / transaminase activity / antibiotic biosynthetic process / pyridoxal phosphate binding Similarity search - Function | |||||||||
Biological species | Bacillus subtilis subsp. subtilis (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.71 Å | |||||||||
Authors | Van Straaten, K.E. / Palmer, D.R.J. / Sanders, D.A.R. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2013 Title: The Structure of NtdA, a Sugar Aminotransferase Involved in the Kanosamine Biosynthetic Pathway in Bacillus subtilis, Reveals a New Subclass of Aminotransferases. Authors: van Straaten, K.E. / Ko, J.B. / Jagdhane, R. / Anjum, S. / Palmer, D.R. / Sanders, D.A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4k2m.cif.gz | 212.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4k2m.ent.gz | 167.3 KB | Display | PDB format |
PDBx/mmJSON format | 4k2m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4k2m_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 4k2m_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 4k2m_validation.xml.gz | 41.7 KB | Display | |
Data in CIF | 4k2m_validation.cif.gz | 64.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k2/4k2m ftp://data.pdbj.org/pub/pdb/validation_reports/k2/4k2m | HTTPS FTP |
-Related structure data
Related structure data | 4k2bSC 4k2iC S: Starting model for refinement C: citing same article (ref.) |
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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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Details | The biological assembly is a homo-dimer |
-Components
#1: Protein | Mass: 50332.648 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis subsp. subtilis (bacteria) Strain: 168 / Gene: 939788, BSU10550, NP_388936.1, ntdA, yhjL / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold (DE3) / References: UniProt: O07566 #2: Sugar | #3: Chemical | ChemComp-EDO / #4: Chemical | #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: 2.57 Å3/Da / Density % sol: 52.05 % |
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Crystal grow | Temperature: 295 K / pH: 5.6 Details: 0.1M tri-sodium citrate pH 5.6, 0.2M ammonium acetate, 10-30% PEG3350, microbatch, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 6, 2011 / Details: MIRRORS |
Radiation | Monochromator: DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 1.71→46.8 Å / Num. obs: 108740 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Biso Wilson estimate: 27.42 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 14.28 |
Reflection shell | Resolution: 1.71→1.75 Å / Rmerge(I) obs: 0.755 / Mean I/σ(I) obs: 2.14 / % possible all: 98.5 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 4K2B Resolution: 1.71→46.73 Å / Occupancy max: 1 / Occupancy min: 0.34 / SU ML: 0.16 / Isotropic thermal model: Isotropic / σ(F): 1.99 / Phase error: 17.73 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.24 Å2 / ksol: 0.4 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.2 Å2
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Refinement step | Cycle: LAST / Resolution: 1.71→46.73 Å
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Refine LS restraints |
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LS refinement shell |
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