+Open data
-Basic information
Entry | Database: PDB / ID: 1ulj | ||||||
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Title | Biphenyl dioxygenase (BphA1A2) in complex with the substrate | ||||||
Components | (biphenyl dioxygenase ...) x 2 | ||||||
Keywords | OXIDOREDUCTASE / alpha3 beta3 hetero hexamer | ||||||
Function / homology | Function and homology information biphenyl 2,3-dioxygenase / biphenyl 2,3-dioxygenase activity / 3-phenylpropionate catabolic process / catabolic process / 2 iron, 2 sulfur cluster binding / iron ion binding Similarity search - Function | ||||||
Biological species | Rhodococcus sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Furusawa, Y. / Nagarajan, V. / Masai, E. / Tanokura, M. / Fukuda, M. / Senda, T. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2004 Title: Crystal Structure of the Terminal Oxygenase Component of Biphenyl Dioxygenase Derived from Rhodococcus sp. Strain RHA1 Authors: Furusawa, Y. / Nagarajan, V. / Tanokura, M. / Masai, E. / Fukuda, M. / Senda, T. #1: Journal: Protein Pept.Lett. / Year: 2003 Title: Crystallization of the terminal oxygenase component of biphenyl dioxygenase derived from Rhodococcus sp. strain RHA1 Authors: Nagarajan, V. / Sakurai, N. / Kubota, M. / Nonaka, T. / Nagumo, H. / Takeda, H. / Nishizaki, T. / Masai, E. / Fukuda, M. / Senda, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ulj.cif.gz | 369.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ulj.ent.gz | 300.9 KB | Display | PDB format |
PDBx/mmJSON format | 1ulj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ulj_validation.pdf.gz | 505.5 KB | Display | wwPDB validaton report |
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Full document | 1ulj_full_validation.pdf.gz | 524.6 KB | Display | |
Data in XML | 1ulj_validation.xml.gz | 64 KB | Display | |
Data in CIF | 1ulj_validation.cif.gz | 88.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ul/1ulj ftp://data.pdbj.org/pub/pdb/validation_reports/ul/1ulj | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Biphenyl dioxygenase ... , 2 types, 6 molecules ACEBDF
#1: Protein | Mass: 51644.566 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodococcus sp. (bacteria) / Strain: RHA1 / Production host: Rhodococcus erythropolis (bacteria) / Strain (production host): IAM1399 / References: UniProt: Q53122, biphenyl 2,3-dioxygenase #2: Protein | Mass: 22049.848 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodococcus sp. (bacteria) / Strain: RHA1 / Production host: Rhodococcus erythropolis (bacteria) / Strain (production host): IAM1399 / References: UniProt: Q53123, biphenyl 2,3-dioxygenase |
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-Non-polymers , 4 types, 308 molecules
#3: Chemical | #4: Chemical | #5: Chemical | #6: 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: 2.7 Å3/Da / Density % sol: 54.13 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: PEG 4000, ammonium acetate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 0.978 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 25, 2002 |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→38 Å / Num. all: 70335 / Num. obs: 70335 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Biso Wilson estimate: 41.6 Å2 / Rmerge(I) obs: 0.101 / Rsym value: 0.101 / Net I/σ(I): 6.7 |
Reflection shell | Resolution: 2.6→2.74 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.357 / Mean I/σ(I) obs: 2.1 / Num. unique all: 10013 / Rsym value: 0.357 / % possible all: 98.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→36.76 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.892 / SU B: 9.694 / SU ML: 0.205 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.737 / ESU R Free: 0.295 / 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: 28.852 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→36.76 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.667 Å / Total num. of bins used: 20 /
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