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Yorodumi- PDB-4npi: 1.94 Angstroms X-ray crystal structure of NAD- and intermediate- ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4npi | ||||||
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Title | 1.94 Angstroms X-ray crystal structure of NAD- and intermediate- bound alpha-aminomuconate-epsilon-semialdehyde dehydrogenase from Pseudomonas fluorescens | ||||||
Components | 2-aminomuconate 6-semialdehyde dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / ALDH / Dehydrogenase / NAD+ | ||||||
Function / homology | Function and homology information polyamine catabolic process / aldehyde dehydrogenase (NAD+) activity / retinal dehydrogenase activity / retinoic acid metabolic process / nucleotide binding Similarity search - Function | ||||||
Biological species | Pseudomonas fluorescens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å | ||||||
Authors | Huo, L. / Davis, I. / Liu, F. / Iwaki, H. / Hasegawa, Y. / Liu, A. | ||||||
Citation | Journal: Nat Commun / Year: 2015 Title: Crystallographic and spectroscopic snapshots reveal a dehydrogenase in action. Authors: Huo, L. / Davis, I. / Liu, F. / Andi, B. / Esaki, S. / Iwaki, H. / Hasegawa, Y. / Orville, A.M. / Liu, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4npi.cif.gz | 411.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4npi.ent.gz | 331.8 KB | Display | PDB format |
PDBx/mmJSON format | 4npi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4npi_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 4npi_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 4npi_validation.xml.gz | 85.8 KB | Display | |
Data in CIF | 4npi_validation.cif.gz | 127.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/np/4npi ftp://data.pdbj.org/pub/pdb/validation_reports/np/4npi | HTTPS FTP |
-Related structure data
Related structure data | 4i1wC 4i25C 4i26C 4i2rSC 4oe2C 4ou2C 4oubC 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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-Components
#1: Protein | Mass: 52120.586 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Gene: nbaE / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q83V33 #2: Chemical | ChemComp-NAD / #3: Chemical | ChemComp-NA / #4: Chemical | ChemComp-2VS / ( #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: 2.62 Å3/Da / Density % sol: 53.03 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9.1 Details: 20% PEG3350, 0.2 M sodium phosphate dibasic, pH 9.1, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 29, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.94→34.73 Å / Num. all: 161090 / Num. obs: 152910 / % possible obs: 94.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.5 % / Rmerge(I) obs: 0.1 |
Reflection shell | Resolution: 1.95→1.98 Å / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 4I2R Resolution: 1.94→109.99 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.945 / Occupancy max: 1 / Occupancy min: 1 / SU B: 3.62 / SU ML: 0.103 / Cross valid method: THROUGHOUT / ESU R: 0.159 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.391 Å2
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Refinement step | Cycle: LAST / Resolution: 1.94→109.99 Å
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Refine LS restraints |
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