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Yorodumi- PDB-9cp7: Crystal structure of DHPS-3-dehydrogenase, HpsN from Cupriavidus ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 9cp7 | ||||||
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Title | Crystal structure of DHPS-3-dehydrogenase, HpsN from Cupriavidus pinatubonensis in complex with product analogue (L-cysteate) and NADH | ||||||
Components | Sulfopropanediol 3-dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / DHPS-3-dehydrogenase | ||||||
Function / homology | Function and homology information sulfopropanediol 3-dehydrogenase / histidinol dehydrogenase activity / L-histidine biosynthetic process / NAD binding / zinc ion binding / cytosol Similarity search - Function | ||||||
Biological species | Cupriavidus pinatubonensis JMP134 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.751 Å | ||||||
Authors | Lee, M. | ||||||
Funding support | Australia, 1items
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Citation | Journal: Chem Sci / Year: 2024 Title: Structural and kinetic insights into the stereospecific oxidation of R -2,3-dihydroxypropanesulfonate by DHPS-3-dehydrogenase from Cupriavidus pinatubonensis. Authors: Burchill, L. / Kaur, A. / Nastasovici, A. / Lee, M. / Williams, S.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 9cp7.cif.gz | 200.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb9cp7.ent.gz | 151.5 KB | Display | PDB format |
PDBx/mmJSON format | 9cp7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 9cp7_validation.pdf.gz | 2.5 MB | Display | wwPDB validaton report |
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Full document | 9cp7_full_validation.pdf.gz | 2.5 MB | Display | |
Data in XML | 9cp7_validation.xml.gz | 43.1 KB | Display | |
Data in CIF | 9cp7_validation.cif.gz | 60.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cp/9cp7 ftp://data.pdbj.org/pub/pdb/validation_reports/cp/9cp7 | HTTPS FTP |
-Related structure data
Related structure data | 8v35C 8v36C 8v37C 9cp8C 9cp9C C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 46991.172 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cupriavidus pinatubonensis JMP134 (bacteria) Gene: hpsN / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q46N53 #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | Has protein modification | N | |
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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: 2.56 Å3/Da / Density % sol: 51.93 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, BIS-TRIS, lithium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95372 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 15, 2024 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95372 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→43.898 Å / Num. obs: 94390 / % possible obs: 99.2 % / Redundancy: 2.9 % / CC1/2: 1 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 1.75→1.78 Å / Mean I/σ(I) obs: 1.7 / Num. unique obs: 4448 / CC1/2: 0.74 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.751→43.898 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.965 / SU B: 2.117 / SU ML: 0.065 / Cross valid method: FREE R-VALUE / ESU R: 0.093 / ESU R Free: 0.091 Details: Hydrogens have been added in their 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 BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.437 Å2
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Refinement step | Cycle: LAST / Resolution: 1.751→43.898 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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