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Yorodumi- PDB-3vsj: Crystal structure of 1,6-APD (2-ANIMOPHENOL-1,6-DIOXYGENASE) comp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3vsj | ||||||
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Title | Crystal structure of 1,6-APD (2-ANIMOPHENOL-1,6-DIOXYGENASE) complexed with intermediate products | ||||||
Components | (2-amino-5-chlorophenol 1,6-dioxygenase ...) x 2 | ||||||
Keywords | OXIDOREDUCTASE / CNBC / 2-HIS-1-CARBOXYLATE FACIAL TRIAD MOTIF / EXTRADIOL DIOXYGENASE | ||||||
Function / homology | Function and homology information 2-amino-5-chlorophenol 1,6-dioxygenase / 2-aminophenol 1,6-dioxygenase / : / dioxygenase activity / ferrous iron binding Similarity search - Function | ||||||
Biological species | Comamonas testosteroni (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Li, D.F. / Hou, Y.J. / Hu, Y. / Wang, D.C. / Liu, W. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2013 Title: Structures of aminophenol dioxygenase in complex with intermediate, product and inhibitor Authors: Li, D.F. / Zhang, J.Y. / Hou, Y.J. / Liu, L. / Hu, Y. / Liu, S.J. / Wang, D.C. / Liu, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3vsj.cif.gz | 251.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3vsj.ent.gz | 200.5 KB | Display | PDB format |
PDBx/mmJSON format | 3vsj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vs/3vsj ftp://data.pdbj.org/pub/pdb/validation_reports/vs/3vsj | HTTPS FTP |
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-Related structure data
Related structure data | 3vsgSC 3vshC 3vsiC 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
-2-amino-5-chlorophenol 1,6-dioxygenase ... , 2 types, 4 molecules ACBD
#1: Protein | Mass: 29298.174 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Comamonas testosteroni (bacteria) / Strain: CNB-1 References: UniProt: Q38M40, UniProt: Q6J1Z5*PLUS, protocatechuate 4,5-dioxygenase #2: Protein | Mass: 35083.070 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Comamonas testosteroni (bacteria) / Strain: CNB-1 References: UniProt: Q38M41, UniProt: Q6J1Z6*PLUS, protocatechuate 4,5-dioxygenase |
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-Non-polymers , 6 types, 1041 molecules
#3: Chemical | ChemComp-CL / | ||||||||
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#4: Chemical | #5: Chemical | ChemComp-2XP / ( | #6: Chemical | ChemComp-2X7 / ( | #7: Chemical | ChemComp-OH / | #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: 2.6 Å3/Da / Density % sol: 52.63 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 25% PEG 3350, 0.2M SODIUM CHLORIDE, PH 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K |
-Data collection
Diffraction | Mean temperature: 98 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 27, 2007 / Details: MIRRORS |
Radiation | Monochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→39.87 Å / Num. all: 59609 / Num. obs: 55311 / % possible obs: 97.76 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Biso Wilson estimate: 31 Å2 / Rmerge(I) obs: 0.109 / Rsym value: 0.109 / Net I/σ(I): 15.7 |
Reflection shell | Resolution: 2.3→2.42 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.456 / Mean I/σ(I) obs: 2.7 / Rsym value: 0.456 / % possible all: 86.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3VSG Resolution: 2.3→39.87 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.903 / SU B: 6.553 / SU ML: 0.16 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(I): 0 / ESU R: 0.358 / ESU R Free: 0.234 / 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: 20.072 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→39.87 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.36 Å / Total num. of bins used: 20
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