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- PDB-1o7g: NAPHTHALENE 1,2-DIOXYGENASE WITH NAPHTHALENE BOUND IN THE ACTIVE SITE. -
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Open data
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Basic information
Entry | Database: PDB / ID: 1o7g | ||||||
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Title | NAPHTHALENE 1,2-DIOXYGENASE WITH NAPHTHALENE BOUND IN THE ACTIVE SITE. | ||||||
![]() | (NAPHTHALENE 1,2-DIOXYGENASE ...![]() | ||||||
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Function / homology | ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Karlsson, A. / Parales, J.V. / Parales, R.E. / Gibson, D.T. / Eklund, H. / Ramaswamy, S. | ||||||
![]() | ![]() Title: Crystal Structure of Naphthalene Dioxygenase: Side-on Binding of Dioxygen to Iron Authors: Karlsson, A. / Parales, J.V. / Parales, R.E. / 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 | ![]() | 154.6 KB | Display | ![]() |
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PDB format | ![]() | 119.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1o7hC ![]() 1o7mC ![]() 1o7nC ![]() 1o7pC ![]() 1o7wC ![]() 1eg9S S: Starting model for refinement C: citing same article ( |
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Similar 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 ACTIVE ENZYME IS A ALPHA3 BETA3 HEXAMER GENERATEDBY THE THREEFOLD |
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Components
-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.) ![]() ![]() ![]() ![]() ![]() References: UniProt: P23094, UniProt: P0A110*PLUS, ![]() |
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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.) ![]() ![]() ![]() ![]() ![]() References: UniProt: P23095, UniProt: P0A112*PLUS, ![]() |
-Non-polymers , 6 types, 531 molecules ![](data/chem/img/EDO.gif)
![](data/chem/img/NPY.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/FES.gif)
![](data/chem/img/FE.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NPY.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/FES.gif)
![](data/chem/img/FE.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-EDO / ![]() #4: Chemical | ChemComp-NPY / | ![]() #5: Chemical | ![]() #6: Chemical | ChemComp-FES / | ![]() #7: Chemical | ChemComp-FE / | ![]() #8: Water | ChemComp-HOH / | ![]() |
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-Details
Compound details | COMPONENT OF NAPHTHALENE DIOXYGENASE (NDO) MULTICOMPONENT ENZYME SYSTEM WHICH CATALYZES THE ...COMPONENT OF NAPHTHALEN |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.56 Å3/Da / Density % sol: 52 % | |||||||||||||||||||||||||
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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 diffusion / Details: Carredano, E., (2000) J. Mol. Biol., 296, 701. | |||||||||||||||||||||||||
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 CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.7→20 Å / Num. obs: 82025 / % possible obs: 95.9 % / Redundancy: 5.49 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 1.7→1.73 Å / Rmerge(I) obs: 0.19 / % possible all: 97.5 |
Reflection | *PLUS Highest resolution: 1.7 Å / Lowest resolution: 20 Å / Num. measured all: 450209 / Rmerge(I) obs: 0.057 |
Reflection shell | *PLUS % possible obs: 95.7 % / Rmerge(I) obs: 0.193 / Mean I/σ(I) obs: 24.4 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 1EG9 Resolution: 1.7→25 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.958 / SU B: 2.269 / SU ML: 0.077 / Cross valid method: THROUGHOUT / ESU R: 0.092 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL PLUS MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.98 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→25 Å
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Refine LS restraints |
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