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Yorodumi- PDB-1nxu: CRYSTAL STRUCTURE OF E. COLI HYPOTHETICAL OXIDOREDUCTASE YIAK NOR... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1nxu | ||||||
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Title | CRYSTAL STRUCTURE OF E. COLI HYPOTHETICAL OXIDOREDUCTASE YIAK NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET ER82. | ||||||
Components | Hypothetical oxidoreductase yiaK | ||||||
Keywords | STRUCTURAL GENOMICS / OXIDOREDUCTASE / Hypothetical protein / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG | ||||||
Function / homology | Function and homology information 3-dehydro-L-gulonate 2-dehydrogenase / 3-dehydro-L-gulonate 2-dehydrogenase activity / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / NAD+ binding / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å | ||||||
Authors | Forouhar, F. / Lee, I. / Benach, J. / Kulkarni, K. / Xiao, R. / Acton, T.B. / Shastry, R. / Rost, B. / Montelione, G.T. / Tong, L. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2004 Title: A Novel NAD-binding Protein Revealed by the Crystal Structure of 2,3-Diketo-L-gulonate Reductase (YiaK). Authors: Forouhar, F. / Lee, I. / Benach, J. / Kulkarni, K. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Tong, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1nxu.cif.gz | 151.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1nxu.ent.gz | 124.7 KB | Display | PDB format |
PDBx/mmJSON format | 1nxu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1nxu_validation.pdf.gz | 453.7 KB | Display | wwPDB validaton report |
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Full document | 1nxu_full_validation.pdf.gz | 469.7 KB | Display | |
Data in XML | 1nxu_validation.xml.gz | 33.8 KB | Display | |
Data in CIF | 1nxu_validation.cif.gz | 50.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nx/1nxu ftp://data.pdbj.org/pub/pdb/validation_reports/nx/1nxu | HTTPS FTP |
-Related 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: 37385.145 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: YIAK OR B3575 / Plasmid: BL21(DE3) / Production host: Escherichia coli (E. coli) References: UniProt: P37672, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor #2: Chemical | ChemComp-SO4 / #3: 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: 1.93 Å3/Da / Density % sol: 35.83 % | |||||||||||||||||||||||||
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Crystal grow | Temperature: 302 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.2 M LiSO4, 19% PEG 3350, 1mM B-NADH, VAPOR DIFFUSION, HANGING DROP, temperature 302K, pH 7.5 | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 29 ℃ | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.97896, 0.9791, 0.9200 | ||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2→37.9 Å / Num. obs: 106854 / % possible obs: 99.3 % / Observed criterion σ(F): 2.6 / Observed criterion σ(I): 2.6 / Redundancy: 3.6 % / Biso Wilson estimate: 9.6 Å2 / Rfree details: 6591 / Limit h max: 30 / Limit h min: 0 / Limit k max: 28 / Limit k min: 0 / Limit l max: 58 / Limit l min: -59 / Observed criterion F max: 34.2 / Observed criterion F min: 2.6 / Rmerge(I) obs: 0.074 / Rsym value: 0.086 / Net I/σ(I): 13.2 | ||||||||||||
Reflection | *PLUS Num. obs: 66809 / % possible obs: 99 % / Num. measured all: 312251 / Rmerge(I) obs: 0.108 | ||||||||||||
Reflection shell | *PLUS % possible obs: 99 % / Rmerge(I) obs: 0.461 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.8→37.9 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2419207.77 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 87.6779 Å2 / ksol: 0.432992 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→37.9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 29 Å / Rfactor Rfree: 0.222 / Rfactor Rwork: 0.182 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.276 / Rfactor Rwork: 0.238 |