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Yorodumi- PDB-4jz6: Crystal structure of a salicylaldehyde dehydrogenase from Pseudom... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4jz6 | ||||||
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Title | Crystal structure of a salicylaldehyde dehydrogenase from Pseudomonas putida G7 complexed with salicylaldehyde | ||||||
Components | Salicylaldehyde dehydrogenase NahF | ||||||
Keywords | OXIDOREDUCTASE / Protein-ligand complex / alpha/beta fold / dehydrogenase / NAD+ Binding / N-terminal 6xHis-tagged protein | ||||||
Function / homology | Function and homology information oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor Similarity search - Function | ||||||
Biological species | Pseudomonas putida (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.417 Å | ||||||
Authors | Coitinho, J.B. / Nagem, R.A.P. | ||||||
Citation | Journal: Biochemistry / Year: 2016 Title: Structural and Kinetic Properties of the Aldehyde Dehydrogenase NahF, a Broad Substrate Specificity Enzyme for Aldehyde Oxidation. Authors: Coitinho, J.B. / Pereira, M.S. / Costa, D.M. / Guimaraes, S.L. / Araujo, S.S. / Hengge, A.C. / Brandao, T.A. / Nagem, R.A. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2012 Title: Expression, purification and preliminary crystallographic studies of NahF, a salicylaldehyde dehydrogenase from Pseudomonas putida G7 involved in naphthalene degradation. Authors: Coitinho, J.B. / Costa, D.M. / Guimaraes, S.L. / de Goes, A.M. / Nagem, R.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4jz6.cif.gz | 215.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4jz6.ent.gz | 171.5 KB | Display | PDB format |
PDBx/mmJSON format | 4jz6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jz/4jz6 ftp://data.pdbj.org/pub/pdb/validation_reports/jz/4jz6 | HTTPS FTP |
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-Related structure data
Related structure data | 1bxsS S: Starting model for refinement |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 54407.832 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: The protein was engineered to contain a 6xHis N-terminal tag Source: (gene. exp.) Pseudomonas putida (bacteria) / Strain: G7 / Gene: nahF / Plasmid: pET28a(TEV) / Production host: Escherichia coli (E. coli) / Strain (production host): Arctic Express / References: UniProt: Q1XGL7, EC: 1.2.1.65 | ||||||
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#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-EDO / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5 Details: Protein at 15 mg/ml. Mother liquor with 1.5 M ammonium sulfate, 5%(v/v) 2-propanol in 100 mM sodium acetate acetic acid buffer pH 5.0., VAPOR DIFFUSION, HANGING DROP, temperature 291K |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.608 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Nov 17, 2011 |
Radiation | Monochromator: Curved crystal of silicon (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.608 Å / Relative weight: 1 |
Reflection | Resolution: 2.417→32.17 Å / Num. obs: 51558 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 3 / Biso Wilson estimate: 18.8 Å2 / Rmerge(I) obs: 0.272 / Net I/σ(I): 10.4 |
Reflection shell | Resolution: 2.417→2.55 Å / Redundancy: 13.2 % / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1BXS Resolution: 2.417→32.168 Å / SU ML: 0.34 / σ(F): 0 / Phase error: 22.4 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 25.779 Å2 / ksol: 0.301 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.417→32.168 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 64.7522 Å / Origin y: -9.6861 Å / Origin z: 13.6149 Å
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Refinement TLS group | Selection details: all |