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Yorodumi- PDB-2hmk: Crystal Structure of Naphthalene 1,2-Dioxygenase Bound to Phenanthrene -
+Open data
-Basic information
Entry | Database: PDB / ID: 2hmk | ||||||
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Title | Crystal Structure of Naphthalene 1,2-Dioxygenase Bound to Phenanthrene | ||||||
Components | (Naphthalene 1,2-dioxygenase ...) x 2 | ||||||
Keywords | OXIDOREDUCTASE / Protein / Rieske Oxygenase | ||||||
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 sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / RIGID BODY REFINEMENT / Resolution: 1.65 Å | ||||||
Authors | Ferraro, D.J. / Okerlund, A.L. / Mowers, J.C. / Ramaswamy, S. | ||||||
Citation | Journal: J.Bacteriol. / Year: 2006 Title: Structural basis for regioselectivity and stereoselectivity of product formation by naphthalene 1,2-dioxygenase. Authors: Ferraro, D.J. / Okerlund, A.L. / Mowers, J.C. / Ramaswamy, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2hmk.cif.gz | 283.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2hmk.ent.gz | 224.8 KB | Display | PDB format |
PDBx/mmJSON format | 2hmk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hm/2hmk ftp://data.pdbj.org/pub/pdb/validation_reports/hm/2hmk | HTTPS FTP |
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-Related structure data
Related structure data | 2hmjC 2hmlC 2hmmC 2hmnC 2hmoC 1o7hS 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 biological assembly is and alpha3 beta3 hexamer. One alpha-beta dimer is in the assymetric unit. The others can be generated by the three-fold axis: y, -x-y, z -x-y, x, z |
-Components
-Naphthalene 1,2-dioxygenase ... , 2 types, 2 molecules AB
#1: Protein | Mass: 49664.355 Da / Num. of mol.: 1 / Mutation: F352V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas sp. (bacteria) / Gene: doxB / Plasmid: pDTG121 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)star / References: UniProt: P0A111, 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 sp. (bacteria) / Gene: doxD / Plasmid: pDTG121 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)star / References: UniProt: P0A113, naphthalene 1,2-dioxygenase |
-Non-polymers , 6 types, 679 molecules
#3: Chemical | ChemComp-FE / | ||||||||
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#4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-FES / | #6: Chemical | ChemComp-PEY / | #7: Chemical | ChemComp-EDO / #8: 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: 2.7 Å3/Da / Density % sol: 54.51 % |
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Crystal grow | Temperature: 279.15 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 1.9-2.2 M Ammonium Sulfate, 4-6% Dioxane, 0.1 M MES, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 279.15K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 9, 2005 |
Radiation | Monochromator: cryogenically-cooled Si(111) double-crystal system Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→39.51 Å / Num. all: 93678 / Num. obs: 93678 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.12 % / Rmerge(I) obs: 0.065 / Χ2: 0.98 / Net I/σ(I): 13.3 / Scaling rejects: 5039 |
Reflection shell | Resolution: 1.65→1.71 Å / Redundancy: 6.63 % / Rmerge(I) obs: 0.306 / Mean I/σ(I) obs: 4.5 / Num. measured all: 62473 / Num. unique all: 9354 / Χ2: 1.34 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: RIGID BODY REFINEMENT Starting model: 1O7H Resolution: 1.65→39.51 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.961 / SU B: 2.645 / SU ML: 0.047 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.103 / ESU R Free: 0.079 / 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 WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.093 Å2
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Refinement step | Cycle: LAST / Resolution: 1.65→39.51 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.65→1.693 Å / Total num. of bins used: 20
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