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Yorodumi- PDB-1uuv: NAPHTHALENE 1,2-DIOXYGENASE WITH NITRIC OXIDE AND INDOLE BOUND IN... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1uuv | ||||||
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Title | NAPHTHALENE 1,2-DIOXYGENASE WITH NITRIC OXIDE AND INDOLE BOUND IN THE ACTIVE SITE. | ||||||
Components | (NAPHTHALENE 1,2-DIOXYGENASE ...) x 2 | ||||||
Keywords | OXIDOREDUCTASE / NON-HEME IRON DIOXYGENASE / ENZYME-SUBSTRATE COMPLEX / AROMATIC HYDROCARBONS CATABOLISM | ||||||
Function / homology | Function and homology information naphthalene 1,2-dioxygenase / naphthalene 1,2-dioxygenase activity / : / dioxygenase activity / 2 iron, 2 sulfur cluster binding / iron ion binding Similarity search - Function | ||||||
Biological species | PSEUDOMONAS PUTIDA (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | Karlsson, A. / Parales, J.V. / Parales, R.E. / Gibson, D.T. / Eklund, H. / Ramaswamy, S. | ||||||
Citation | Journal: J.Biol.Inorg.Chem. / Year: 2005 Title: No Binding to Naphthalene Dioxygenase. 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 | 1uuv.cif.gz | 153.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1uuv.ent.gz | 118.6 KB | Display | PDB format |
PDBx/mmJSON format | 1uuv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uu/1uuv ftp://data.pdbj.org/pub/pdb/validation_reports/uu/1uuv | HTTPS FTP |
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-Related structure data
Related structure data | 1uuwC 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 ALPHA3BETA3 HEXAMERGENERATED BY 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: NCIB9816-4 / Plasmid: PDTG14 / 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: NCIB9816-4 / Plasmid: PDTG14 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): JM109(DE3) References: UniProt: P23095, UniProt: P0A112*PLUS, naphthalene 1,2-dioxygenase |
-Non-polymers , 7 types, 475 molecules
#3: Chemical | ChemComp-FES / | ||||||||||
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#4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-IND / | #6: Chemical | ChemComp-NO / | #7: Chemical | ChemComp-FE / | #8: Chemical | #9: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 52.3 % |
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Crystal grow | pH: 6 Details: AMMONIUM SULPHATE 2M, MES 0.1M, DIOXANE 2-3%, pH 6.00 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.93 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.93 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→25 Å / Num. obs: 92741 / % possible obs: 98.3 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 15.8 |
Reflection shell | Resolution: 1.6→1.71 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.195 / % possible all: 98 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1EG9 Resolution: 1.65→25 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.964 / SU B: 2.446 / SU ML: 0.085 / Cross valid method: THROUGHOUT / ESU R: 0.091 / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS THE RESIDUES ASP 448, ARG 449 AND MET 501 WERE NOT INCLUDED IN THE SEARCH-MODEL AND NO DENSITY CAN BE SEEN FOR THESE RESIDUES IN THE MAP.
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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: 29.24 Å2
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Refinement step | Cycle: LAST / Resolution: 1.65→25 Å
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Refine LS restraints |
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