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- PDB-6dll: 2.2 Angstrom Resolution Crystal Structure of P-Hydroxybenzoate Hy... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6dll | |||||||||
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Title | 2.2 Angstrom Resolution Crystal Structure of P-Hydroxybenzoate Hydroxylase from Pseudomonas putida in Complex with FAD. | |||||||||
![]() | p-hydroxybenzoate hydroxylase | |||||||||
![]() | OXIDOREDUCTASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / P-hydroxybenzoate Hydroxylase / FAD | |||||||||
Function / homology | ![]() benzoate catabolic process / 4-hydroxybenzoate 3-monooxygenase / 4-hydroxybenzoate 3-monooxygenase activity / FAD binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Minasov, G. / Shuvalova, L. / Kiryukhina, O. / Dubrovska, I. / Grimshaw, S. / Kwon, K. / Anderson, W.F. / Satchell, K.J.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID) | |||||||||
![]() | ![]() Title: Structural comparison of p-hydroxybenzoate hydroxylase (PobA) from Pseudomonas putida with PobA from other Pseudomonas spp. and other monooxygenases. Authors: Lazar, J.T. / Shuvalova, L. / Rosas-Lemus, M. / Kiryukhina, O. / Satchell, K.J.F. / Minasov, G. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 667.8 KB | Display | ![]() |
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PDB format | ![]() | 555.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 68.3 KB | Display | |
Data in CIF | ![]() | 97 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1pbbS S: Starting model for refinement |
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Similar structure data | |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 44590.676 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 47054 / DSM 6125 / NCIMB 11950 / KT2440 / Gene: pobA, PP_3537 / Plasmid: pMCSG53 / Production host: ![]() ![]() References: UniProt: Q88H28, 4-hydroxybenzoate 3-monooxygenase #2: Chemical | ChemComp-FAD / #3: Chemical | ChemComp-CL / #4: Chemical | ChemComp-FMT / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.7 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: Protein: 13.8 mg/ml, 0.01M Tris HCl (pH 8.3), 1mM FAD; Screen: PACT (F4), 0.2M Potassium thiocyanate, 0.1M Bis-Tris propane (pH 6.5), 20% (w/v) PEG 3350. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 22, 2016 / Details: C(111) |
Radiation | Monochromator: BERYLLIUM LENSES / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→30 Å / Num. obs: 86948 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Biso Wilson estimate: 44.8 Å2 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.031 / Rrim(I) all: 0.067 / Rsym value: 0.059 / Χ2: 1.011 / Net I/σ(I): 23.8 |
Reflection shell | Resolution: 2.2→2.24 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.805 / Mean I/σ(I) obs: 1.94 / Num. unique obs: 4317 / CC1/2: 0.779 / Rpim(I) all: 0.431 / Rrim(I) all: 0.915 / Rsym value: 0.805 / Χ2: 1.006 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1PBB Resolution: 2.2→29.61 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.942 / SU B: 11.718 / SU ML: 0.158 / Cross valid method: THROUGHOUT / ESU R: 0.282 / ESU R Free: 0.207 / 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: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.517 Å2
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Refinement step | Cycle: 1 / Resolution: 2.2→29.61 Å
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Refine LS restraints |
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