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- PDB-1eg9: NAPHTHALENE 1,2-DIOXYGENASE WITH INDOLE BOUND IN THE ACTIVE SITE. -
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Open data
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Basic information
Entry | Database: PDB / ID: 1eg9 | ||||||
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Title | NAPHTHALENE 1,2-DIOXYGENASE WITH INDOLE BOUND IN THE ACTIVE SITE. | ||||||
![]() | (PROTEIN (NAPHTHALENE 1,2-DIOXYGENASE ...) x 2 | ||||||
![]() | OXIDOREDUCTASE / NON-HEME IRON DIOXYGENASE / ENZYME-SUBSTRATE COMPLEX | ||||||
Function / homology | ![]() naphthalene 1,2-dioxygenase / naphthalene 1,2-dioxygenase activity / 3-phenylpropionate catabolic process / : / dioxygenase activity / 2 iron, 2 sulfur cluster binding / iron ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Carredano, E. / Karlsson, A. / Kauppi, B. / Choudhury, D. / Parales, R.E. / Parales, J.V. / Lee, K. / Gibson, D.T. / Eklund, H. / Ramaswamy, S. | ||||||
![]() | ![]() Title: Substrate binding site of naphthalene 1,2-dioxygenase: functional implications of indole binding. Authors: Carredano, E. / Karlsson, A. / Kauppi, B. / Choudhury, D. / Parales, R.E. / Parales, J.V. / Lee, K. / Gibson, D.T. / Eklund, H. / Ramaswamy, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 155.4 KB | Display | ![]() |
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PDB format | ![]() | 120.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 465.6 KB | Display | ![]() |
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Full document | ![]() | 479.9 KB | Display | |
Data in XML | ![]() | 32.1 KB | Display | |
Data in CIF | ![]() | 48 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Details | THE ACTIVE ENZYME IS A ALPHA3BETA3 HEXAMER GENERATED BY THE THREEFOLD. |
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Components
-PROTEIN (NAPHTHALENE 1,2-DIOXYGENASE ... , 2 types, 2 molecules AB
#1: Protein | Mass: 49664.355 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein | Mass: 22969.088 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Non-polymers , 5 types, 618 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/FE.gif)
![](data/chem/img/FES.gif)
![](data/chem/img/IND.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/FE.gif)
![](data/chem/img/FES.gif)
![](data/chem/img/IND.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | ChemComp-FE / | #5: Chemical | ChemComp-FES / | #6: Chemical | ChemComp-IND / | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.72 Å3/Da / Density % sol: 54.82 % | |||||||||||||||||||||||||
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Crystal grow | pH: 6 Details: AMMONIUM SULPHATE 2M, MES 0.1M, DIOXANE 2-3%, pH 6.00 | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 8 ℃ / Method: vapor diffusionDetails: drop consists of equal volume of protein and reservoir solutions | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4r / Detector: CCD / Date: Dec 5, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.93 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→20 Å / Num. obs: 896312 / % possible obs: 99.9 % / Redundancy: 8.8 % / Biso Wilson estimate: 16.8 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 1.6→20 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.307 / % possible all: 99 |
Reflection | *PLUS Num. obs: 102843 / Num. measured all: 896312 |
Reflection shell | *PLUS Lowest resolution: 1.63 Å / % possible obs: 99 % / Mean I/σ(I) obs: 3.31 |
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Processing
Software |
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Refinement | Resolution: 1.6→20 Å
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Refinement step | Cycle: LAST / Resolution: 1.6→20 Å
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||
Refine LS restraints | *PLUS
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