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Yorodumi- PDB-1nvm: Crystal structure of a bifunctional aldolase-dehydrogenase : sequ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1nvm | ||||||
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Title | Crystal structure of a bifunctional aldolase-dehydrogenase : sequestering a reactive and volatile intermediate | ||||||
Components |
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Keywords | LYASE/OXIDOREDUCTASE / Sequestered tunnel / substrate channeling / Bifunctional enzyme / LYASE-OXIDOREDUCTASE COMPLEX | ||||||
Function / homology | Function and homology information phenol-containing compound catabolic process / 4-hydroxy-2-oxovalerate aldolase / 4-hydroxy-2-oxovalerate aldolase activity / acetaldehyde dehydrogenase (acetylating) / acetaldehyde dehydrogenase (acetylating) activity / benzoate catabolic process via hydroxylation / : / NAD binding / NADP binding / manganese ion binding Similarity search - Function | ||||||
Biological species | Pseudomonas sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å | ||||||
Authors | Manjasetty, A.B. / Powlowski, J. / Vrielink, A. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2003 Title: Crystal structure of a bifunctional aldolase-dehydrogenase: Sequestering a reactive and volatile intermediate Authors: Manjasetty, A.B. / Powlowski, J. / Vrielink, A. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2001 Title: Crystallization and preliminary X-ray analysis of dmpFG-encoded 4-hydroxy-2-ketovalerate aldolase-aldehyde dehydrogenase (acylating) from Pseudomonas sp.strain CF600 | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1nvm.cif.gz | 559.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1nvm.ent.gz | 451 KB | Display | PDB format |
PDBx/mmJSON format | 1nvm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1nvm_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 1nvm_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 1nvm_validation.xml.gz | 128 KB | Display | |
Data in CIF | 1nvm_validation.cif.gz | 187.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nv/1nvm ftp://data.pdbj.org/pub/pdb/validation_reports/nv/1nvm | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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3 |
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Unit cell |
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-Components
-Protein , 2 types, 8 molecules ACEGBDFH
#1: Protein | Mass: 37520.645 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas sp. (bacteria) / Strain: CF600 / Gene: DMPG / Plasmid: pT7-5 / Production host: Escherichia coli (E. coli) References: UniProt: P51016, Lyases; Carbon-carbon lyases; Oxo-acid-lyases #2: Protein | Mass: 32713.812 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas sp. (bacteria) / Strain: CF600 / Gene: DMPF / Plasmid: pT7-5 / Production host: Escherichia coli (E. coli) References: UniProt: Q52060, acetaldehyde dehydrogenase (acetylating) |
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-Non-polymers , 6 types, 2840 molecules
#3: Chemical | ChemComp-MN / #4: Chemical | ChemComp-OXL / #5: Chemical | ChemComp-SO4 / #6: Chemical | ChemComp-MPD / ( #7: Chemical | #8: 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: 2.16 Å3/Da / Density % sol: 42.73 % / Description: 112 SE SUBSTRUCTURE | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 310 K / pH: 7.5 Details: PEG 8000, Ammonium sulfate, PIPES, pH 7.5, Hanging drop and micro seeding, temperature 310.0K, pH 7.50 | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 290 K / pH: 7.4 / Method: vapor diffusion, hanging dropDetails: Manjasetty, B.A., (2001) Acta Crystallogr.,Sect.D, 57, 582. | ||||||||||||||||||||||||||||||||||||||||||
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: ALS / Beamline: 5.0.2 / Wavelength: 1 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 14, 2000 / Details: MIRRORS |
Radiation | Monochromator: CURVED-CRYSTAL SI 111 / Protocol: MULTIPLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→100 Å / Num. obs: 299052 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Biso Wilson estimate: 28.3 Å2 / Rmerge(I) obs: 0.078 / Rsym value: 0.078 / Net I/σ(I): 18.7 |
Reflection shell | Resolution: 1.7→1.74 Å / Redundancy: 4 % / Rmerge(I) obs: 0.565 / Mean I/σ(I) obs: 2 / Rsym value: 0.565 / % possible all: 99.3 |
Reflection | *PLUS Highest resolution: 1.7 Å / Num. measured all: 1829280 |
Reflection shell | *PLUS % possible obs: 99.3 % / Mean I/σ(I) obs: 2 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.7→20 Å / Isotropic thermal model: Isotropic / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: MAXIMUM LIKLIHOOD METHOD
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Displacement parameters | Biso mean: 28.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.783 Å /
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Refinement | *PLUS Highest resolution: 1.7 Å / Lowest resolution: 20 Å / Rfactor Rfree: 0.232 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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