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Yorodumi- PDB-5d2k: 4-oxalocrotonate decarboxylase from Pseudomonas putida G7 - compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5d2k | |||||||||||||||
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Title | 4-oxalocrotonate decarboxylase from Pseudomonas putida G7 - complexed with magnesium and 2-oxoadipate | |||||||||||||||
Components | 4-oxalocrotonate decarboxylase NahK | |||||||||||||||
Keywords | LYASE / naphthalene degradation | |||||||||||||||
Function / homology | Function and homology information | |||||||||||||||
Biological species | Pseudomonas putida (bacteria) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.571 Å | |||||||||||||||
Authors | Guimaraes, S.L. / Nagem, R.A.P. | |||||||||||||||
Funding support | Brazil, 4items
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Citation | Journal: Biochemistry / Year: 2016 Title: Crystal Structures of Apo and Liganded 4-Oxalocrotonate Decarboxylase Uncover a Structural Basis for the Metal-Assisted Decarboxylation of a Vinylogous beta-Keto Acid. Authors: Guimaraes, S.L. / Coitinho, J.B. / Costa, D.M. / Araujo, S.S. / Whitman, C.P. / 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 | 5d2k.cif.gz | 135.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5d2k.ent.gz | 102.6 KB | Display | PDB format |
PDBx/mmJSON format | 5d2k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d2/5d2k ftp://data.pdbj.org/pub/pdb/validation_reports/d2/5d2k | HTTPS FTP |
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-Related structure data
Related structure data | 5d2fC 5d2gC 5d2hC 5d2iC 5d2jC 2eb4S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 28934.121 Da / Num. of mol.: 2 / Mutation: L155P Source method: isolated from a genetically manipulated source Details: from plasmid NAH7 / Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: nahK / Plasmid: pET28a-TEV Details (production host): The thrombin site in the original pET28a vector was replaced by the TEV site for tag cleavage Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q1XGK3, 2-oxo-3-hexenedioate decarboxylase |
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-Non-polymers , 5 types, 662 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-ACT / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.57 % / Description: needle-shaped |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: sodium acetate trihydrate, PEG 4000 / PH range: 8.5 - 10.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.461 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 17, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.461 Å / Relative weight: 1 |
Reflection | Resolution: 1.571→40.78 Å / Num. obs: 69868 / % possible obs: 99.9 % / Redundancy: 5.5 % / Biso Wilson estimate: 13.25 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 29.704 |
Reflection shell | Resolution: 1.571→1.6 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.177 / Mean I/σ(I) obs: 7.972 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2EB4 Resolution: 1.571→40.78 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.37 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.34 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.571→40.78 Å
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Refine LS restraints |
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LS refinement shell |
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