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Yorodumi- PDB-4go4: Crystal structure of PnpE in complex with Nicotinamide adenine di... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4go4 | ||||||
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Title | Crystal structure of PnpE in complex with Nicotinamide adenine dinucleotide | ||||||
Components | Putative gamma-hydroxymuconic semialdehyde dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / gamma-hydroxymuconic semialdehyde dehydrogenase | ||||||
Function / homology | Function and homology information oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor / organic substance metabolic process / nucleotide binding Similarity search - Function | ||||||
Biological species | Pseudomonas (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.099 Å | ||||||
Authors | Su, J. / Zhang, C. / Liu, S. / Zhu, D. / Gu, L. | ||||||
Citation | Journal: To be Published Title: Crystal structure of PnpE in complex with Nicotinamide adenine dinucleotide Authors: Su, J. / Zhang, C. / Liu, S. / Zhu, D. / Gu, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4go4.cif.gz | 722.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4go4.ent.gz | 605.1 KB | Display | PDB format |
PDBx/mmJSON format | 4go4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/go/4go4 ftp://data.pdbj.org/pub/pdb/validation_reports/go/4go4 | HTTPS FTP |
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-Related structure data
Related structure data | 4go3S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 53421.758 Da / Num. of mol.: 8 / Mutation: S426H, Y484H Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas (bacteria) / Strain: WBC-3 / Gene: pnpE / Plasmid: pET29b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C1I208, aldehyde dehydrogenase (NAD+) #2: Chemical | ChemComp-NAD / #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: 2.24 Å3/Da / Density % sol: 45.2 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.1M BICINE pH 8.5, 20% PEG 10000, 1mM NAD, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å | ||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 10, 2010 | ||||||||||||||||||
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 | ||||||||||||||||||
Reflection | Resolution: 3→50 Å / Num. all: 69131 / Num. obs: 69131 / % possible obs: 91.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 62.6 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 15.5 | ||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4GO3 Resolution: 3.099→37.243 Å / Occupancy max: 1 / Occupancy min: 0.39 / SU ML: 0.38 / σ(F): 0 / Phase error: 26.09 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 10.933 Å2 / ksol: 0.289 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 153.48 Å2 / Biso mean: 60.26 Å2 / Biso min: 12.76 Å2
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Refinement step | Cycle: LAST / Resolution: 3.099→37.243 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: 13
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