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Yorodumi- PDB-2imf: 2-Hydroxychromene-2-carboxylate Isomerase: a Kappa Class Glutathi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2imf | ||||||
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Title | 2-Hydroxychromene-2-carboxylate Isomerase: a Kappa Class Glutathione-S-Transferase from Pseudomonas putida | ||||||
Components | 2-hydroxychromene-2-carboxylate isomerase | ||||||
Keywords | TRANSFERASE / isomerase / glutathione / kgst / kappa gst | ||||||
Function / homology | Function and homology information 2-hydroxychromene-2-carboxylate isomerase / 2-hydroxychromene-2-carboxylate isomerase activity / naphthalene catabolic process / oxidoreductase activity Similarity search - Function | ||||||
Biological species | Pseudomonas putida (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å | ||||||
Authors | Thompson, L.C. / Ladner, J.E. / Codreanu, S.G. / Harp, J. / Gilliland, G.L. / Armstrong, R.N. | ||||||
Citation | Journal: Biochemistry / Year: 2007 Title: 2-Hydroxychromene-2-carboxylic acid isomerase: a kappa class glutathione transferase from Pseudomonas putida. Authors: Thompson, L.C. / Ladner, J.E. / Codreanu, S.G. / Harp, J. / Gilliland, G.L. / Armstrong, R.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2imf.cif.gz | 63 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2imf.ent.gz | 45.9 KB | Display | PDB format |
PDBx/mmJSON format | 2imf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/im/2imf ftp://data.pdbj.org/pub/pdb/validation_reports/im/2imf | HTTPS FTP |
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-Related 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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Details | The second part of the biological dimer is generated by -x,-y,z |
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 23083.174 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: nahD / Plasmid: pET20b(+) / Production host: Escherichia coli (E. coli) / References: UniProt: Q51948, glutathione transferase |
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-Non-polymers , 5 types, 255 molecules
#2: Chemical | #3: Chemical | ChemComp-GSH / | #4: Chemical | ChemComp-TOM / | #5: Chemical | ChemComp-CXS / | #6: 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: 2.26 Å3/Da / Density % sol: 45.51 % |
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Crystal grow | Temperature: 294 K / Method: microbatch under oil / pH: 6.1 Details: crystallization solution: 1.2M sodium dihydrogen phosphate, 0.8M potassium hydrogen phosphate,0.2M lithium sulfate, 0.1M CAPS pH 6.1. Protein and crystallization solutions were mixed 1:1., ...Details: crystallization solution: 1.2M sodium dihydrogen phosphate, 0.8M potassium hydrogen phosphate,0.2M lithium sulfate, 0.1M CAPS pH 6.1. Protein and crystallization solutions were mixed 1:1., microbatch under oil, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Detector: CCD / Date: Jun 20, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→24.75 Å / Num. obs: 43839 / % possible obs: 87.4 % / Redundancy: 12.6 % / Rmerge(I) obs: 0.054 |
Reflection shell | Resolution: 1.3→1.35 Å / Rmerge(I) obs: 0.334 / Mean I/σ(I) obs: 2 / Num. unique all: 2694 / % possible all: 52.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→24.75 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.953 / SU B: 0.932 / SU ML: 0.04 / Cross valid method: THROUGHOUT / ESU R: 0.062 / ESU R Free: 0.064 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.974 Å2
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Refinement step | Cycle: LAST / Resolution: 1.3→24.75 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.3→1.37 Å / Total num. of bins used: 10
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