+Open data
-Basic information
Entry | Database: PDB / ID: 1o7m | ||||||
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Title | NAPHTHALENE 1,2-DIOXYGENASE, BINARY COMPLEX WITH DIOXYGEN | ||||||
Components | (NAPHTHALENE 1,2-DIOXYGENASE ...) x 2 | ||||||
Keywords | OXIDOREDUCTASE / NON-HEME IRON DIOXYGENASE / ENZYME-SUBSTRATE COMPLEX / IRON-SULFUR / AROMATIC HYDROCARBON CATABOLISM | ||||||
Function / homology | Function and homology information 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 | PSEUDOMONAS PUTIDA (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Karlsson, A. / Parales, J.V. / Parales, R.E. / Gibson, D.T. / Eklund, H. / Ramaswamy, S. | ||||||
Citation | Journal: Science / Year: 2003 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1o7m.cif.gz | 154.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1o7m.ent.gz | 119.9 KB | Display | PDB format |
PDBx/mmJSON format | 1o7m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o7/1o7m ftp://data.pdbj.org/pub/pdb/validation_reports/o7/1o7m | HTTPS FTP |
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-Related structure data
Related structure data | 1o7gC 1o7hC 1o7nC 1o7pC 1o7wC 1eg9S S: Starting model for refinement C: citing same article (ref.) |
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Similar 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 ACTIVE ENZYME IS A ALPHA3 BETA3 HEXAMER GENERATEDBY THE THREEFOLD |
-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.) PSEUDOMONAS PUTIDA (bacteria) / Strain: NCIB 9816-4 / Plasmid: PDTG141 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): JM109(DE3) References: UniProt: P23094, UniProt: P0A110*PLUS, naphthalene 1,2-dioxygenase |
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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.) PSEUDOMONAS PUTIDA (bacteria) / Strain: NCIB 9816-4 / Plasmid: PDTG141 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): JM109(DE3) References: UniProt: P23095, UniProt: P0A112*PLUS, naphthalene 1,2-dioxygenase |
-Non-polymers , 6 types, 565 molecules
#3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-OXY / | #5: Chemical | #6: Chemical | ChemComp-FES / | #7: Chemical | ChemComp-FE / | #8: 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: 2.56 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: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.54 |
Detector | Type: RIGAKU MSC / Detector: IMAGE PLATE / Date: Dec 15, 2001 / Details: CONFOCAL MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→30 Å / Num. obs: 80092 / % possible obs: 94 % / Redundancy: 3.67 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 10.2 |
Reflection shell | Resolution: 1.75→1.79 Å / Rmerge(I) obs: 0.321 / Mean I/σ(I) obs: 2.2 / % possible all: 86.5 |
Reflection | *PLUS Lowest resolution: 30 Å / Num. measured all: 293928 |
Reflection shell | *PLUS % possible obs: 86.5 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1EG9 Resolution: 1.75→30 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.611 / SU ML: 0.086 / Cross valid method: THROUGHOUT / ESU R: 0.101 / ESU R Free: 0.089 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ASN 363 AND MET 366 HAVE BEEN MODELLED WITH DOUBLE CONFORMATIONS.
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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: 14.3 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→30 Å
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Refine LS restraints |
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