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Yorodumi- PDB-3mfl: Axial Ligand Swapping In Double Mutant Maintains Intradiol-cleava... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3mfl | ||||||
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Title | Axial Ligand Swapping In Double Mutant Maintains Intradiol-cleavage Chemistry in Protocatechuate 3,4-Dioxygenase | ||||||
Components | (Protocatechuate 3,4-dioxygenase ...) x 2 | ||||||
Keywords | OXIDOREDUCTASE / dioxygenase / non-heme / iron / homoprotocatechuate / intradiol / substrate analogue | ||||||
Function / homology | Function and homology information protocatechuate 3,4-dioxygenase / protocatechuate 3,4-dioxygenase activity / 3,4-dihydroxybenzoate catabolic process / beta-ketoadipate pathway / ferric iron binding Similarity search - Function | ||||||
Biological species | Pseudomonas putida (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.78 Å | ||||||
Authors | Purpero, V.M. / Lipscomb, J.D. | ||||||
Citation | Journal: To be Published Title: Axial Ligand Swapping In Double Mutant Maintains Intradiol-cleavage Chemistry in Protocatechuate 3,4-Dioxygenase Authors: Purpero, V.M. / Lipscomb, J.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3mfl.cif.gz | 298.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3mfl.ent.gz | 238.3 KB | Display | PDB format |
PDBx/mmJSON format | 3mfl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mf/3mfl ftp://data.pdbj.org/pub/pdb/validation_reports/mf/3mfl | HTTPS FTP |
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-Related structure data
Related structure data | 3mi1C 3mi5C 3mv4C 3mv6C 3t63C 3t67C 3ini 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 | exists as a dodecamer (12) of dimer in solution. This space group (I222) shows 3 dimers per asymmetric unit (x,y,z), therefore applying the symmetry operators (-x,y,-z), (x,-y,-z) and (-x,-y,z) yields the biological assembly |
-Components
-Protocatechuate 3,4-dioxygenase ... , 2 types, 6 molecules ABCMNO
#1: Protein | Mass: 22278.812 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: pcaG / Plasmid: pCE vector, pT7-7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) References: UniProt: P00436, protocatechuate 3,4-dioxygenase #2: Protein | Mass: 26696.287 Da / Num. of mol.: 3 / Mutation: Y148H, H163Y Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: pcaH / Plasmid: pCE vector, pT7-7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) References: UniProt: P00437, protocatechuate 3,4-dioxygenase |
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-Non-polymers , 8 types, 1069 molecules
#3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-GOL / #5: Chemical | #6: Chemical | #7: Chemical | ChemComp-CO3 / | #8: Chemical | #9: Chemical | ChemComp-CL / | #10: 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: 2.58 Å3/Da / Density % sol: 52.41 % |
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Crystal grow | Temperature: 277 K / pH: 8.5 Details: 1.5-1.8 M ammonium sulfate, 40-60 mM Tris buffer pH 8.5, 5 mM BME, with varying ML to enzyme ratios 1:2 to 4:1, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.98 |
Detector | Type: SBC-3 / Detector: CCD / Date: Nov 24, 2008 / Details: MIRRORS |
Radiation | Monochromator: SAGITALLY FOCUSING DOUBLE CRYSTA / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.78→50 Å / Num. obs: 145553 / % possible obs: 99.8 % / Observed criterion σ(I): 3 / Redundancy: 6.3 % / Biso Wilson estimate: 17.9 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 1.78→1.81 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.408 / Mean I/σ(I) obs: 3.96 / % possible all: 100 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.78→23.87 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.95 / Occupancy max: 1 / Occupancy min: 0.1 / SU B: 1.902 / SU ML: 0.061 / SU R Cruickshank DPI: 0.102 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.102 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING
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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: 20.78 Å2
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Refinement step | Cycle: LAST / Resolution: 1.78→23.87 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.78→1.82 Å / Total num. of bins used: 20
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