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- PDB-2imd: Structure of SeMet 2-hydroxychromene-2-carboxylate isomerase (HCC... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2imd | ||||||
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Title | Structure of SeMet 2-hydroxychromene-2-carboxylate isomerase (HCCA isomerase) | ||||||
![]() | 2-hydroxychromene-2-carboxylate isomerase | ||||||
![]() | TRANSFERASE / isomerase / glutathione / kgst / kappa gst | ||||||
Function / homology | ![]() 2-hydroxychromene-2-carboxylate isomerase / 2-hydroxychromene-2-carboxylate isomerase activity / naphthalene catabolic process / glutathione peroxidase activity / glutathione transferase activity / glutathione metabolic process / peroxisome Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() | ||||||
![]() | Thompson, L.C. / Ladner, J.E. / Codreanu, S.G. / Harp, J. / Gilliland, G.L. / Armstrong, R.N. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 58.7 KB | Display | ![]() |
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PDB format | ![]() | 47.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 976.7 KB | Display | ![]() |
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Full document | ![]() | 983.7 KB | Display | |
Data in XML | ![]() | 14 KB | Display | |
Data in CIF | ![]() | 20.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Details | The second part of the biological dimer is generated by -x,-y,z |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 23364.543 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 6 types, 221 molecules ![](data/chem/img/PO4.gif)
![](data/chem/img/GSH.gif)
![](data/chem/img/TOH.gif)
![](data/chem/img/2C2.gif)
![](data/chem/img/CXS.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GSH.gif)
![](data/chem/img/TOH.gif)
![](data/chem/img/2C2.gif)
![](data/chem/img/CXS.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-GSH / | #4: Chemical | ChemComp-TOH / ( | #5: Chemical | ChemComp-2C2 / ( | #6: Chemical | ChemComp-CXS / | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.75 % |
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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: ![]() |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 7, 2004 / Details: BLUE MAX-FLUX CONFOCAL |
Radiation | Monochromator: CONFOCAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→27 Å / Num. all: 34098 / Num. obs: 34098 / % possible obs: 99.4 % / Redundancy: 3.83 % / Rmerge(I) obs: 0.044 |
Reflection shell | Resolution: 1.5→1.55 Å / Redundancy: 2.27 % / Rmerge(I) obs: 0.291 / Mean I/σ(I) obs: 2.2 / Num. unique all: 6066 |
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Processing
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Refinement | Method to determine structure: SAD plus SIR / Resolution: 1.6→20 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.947 / SU B: 1.965 / SU ML: 0.07 / Cross valid method: THROUGHOUT / ESU R: 0.099 / ESU R Free: 0.101 / 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: 22.331 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.686 Å / Total num. of bins used: 10
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