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Yorodumi- PDB-2gbx: Crystal Structure of Biphenyl 2,3-Dioxygenase from Sphingomonas y... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2gbx | ||||||
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Title | Crystal Structure of Biphenyl 2,3-Dioxygenase from Sphingomonas yanoikuyae B1 Bound to Biphenyl | ||||||
Components | (Biphenyl 2,3-Dioxygenase ...) x 2 | ||||||
Keywords | OXIDOREDUCTASE / RIESKE OXYGENASE / NON HEME IRON / DIOXYGENASE | ||||||
Function / homology | Function and homology information 3-phenylpropionate catabolic process / : / dioxygenase activity / 2 iron, 2 sulfur cluster binding / iron ion binding / metal ion binding Similarity search - Function | ||||||
Biological species | Sphingobium yanoikuyae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Ferraro, D.J. / Brown, E.N. / Yu, C. / Parales, R.E. / Gibson, D.T. / Ramaswamy, S. | ||||||
Citation | Journal: Bmc Struct.Biol. / Year: 2007 Title: Structural investigations of the ferredoxin and terminal oxygenase components of the biphenyl 2,3-dioxygenase from Sphingobium yanoikuyae B1. Authors: Ferraro, D.J. / Brown, E.N. / Yu, C.L. / Parales, R.E. / Gibson, D.T. / Ramaswamy, S. | ||||||
History |
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Remark 999 | SEQUENCE According to authors, there is no aminoacid sequence database reference available for the protein |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2gbx.cif.gz | 359.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2gbx.ent.gz | 294.2 KB | Display | PDB format |
PDBx/mmJSON format | 2gbx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2gbx_validation.pdf.gz | 511.9 KB | Display | wwPDB validaton report |
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Full document | 2gbx_full_validation.pdf.gz | 541.8 KB | Display | |
Data in XML | 2gbx_validation.xml.gz | 65.9 KB | Display | |
Data in CIF | 2gbx_validation.cif.gz | 89.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gb/2gbx ftp://data.pdbj.org/pub/pdb/validation_reports/gb/2gbx | HTTPS FTP |
-Related structure data
Related structure data | 2gbwSC 2i7fC 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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Details | The alpha-3 beta-3 assembly is the biological assembly, and is fully contained in the assymetric unit. |
-Components
-Biphenyl 2,3-Dioxygenase ... , 2 types, 6 molecules ACEBDF
#1: Protein | Mass: 51036.898 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sphingobium yanoikuyae (bacteria) / Strain: B1 / Gene: bphA1fA2f / Plasmid: pET101D / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A2TC87 #2: Protein | Mass: 20786.336 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sphingobium yanoikuyae (bacteria) / Plasmid: pET101D / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A2TC88 |
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-Non-polymers , 5 types, 205 molecules
#3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-ZN / #7: 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: 2.64 Å3/Da / Density % sol: 53.45 % |
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Crystal grow | Temperature: 277.15 K / pH: 6.8 Details: 20% PEG3350, 1.0 M Sodium Chloride, 0.037M Zinc Chloride, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K, pH 6.80 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD |
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: 2.8→19.481 Å / Num. all: 56587 / Num. obs: 56587 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 47.22 Å2 |
Reflection shell | Resolution: 2.8→3 Å / Rmerge(I) obs: 0.269 / Mean I/σ(I) obs: 6.3 / % possible all: 98.7 |
-Phasing
Phasing MR | Rfactor: 0.322 / Cor.coef. Fo:Fc: 0.734 / Cor.coef. Io to Ic: 0.736
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-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2GBW Resolution: 2.8→19.48 Å / Cor.coef. Fo:Fc: 0.896 / Cor.coef. Fo:Fc free: 0.863 / SU B: 33.994 / SU ML: 0.323 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.58 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→19.48 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.87 Å
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