[English] 日本語
Yorodumi- PDB-3mi1: Axial Ligand Swapping In Double Mutant Maintains Intradiol-cleava... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3mi1 | ||||||
---|---|---|---|---|---|---|---|
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 | ||||||
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: 1.74 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3mi1.cif.gz | 306.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3mi1.ent.gz | 245.1 KB | Display | PDB format |
PDBx/mmJSON format | 3mi1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mi/3mi1 ftp://data.pdbj.org/pub/pdb/validation_reports/mi/3mi1 | HTTPS FTP |
---|
-Related structure data
Related structure data | 3mflC 3mi5C 3mv4C 3mv6C 3t63C 3t67C C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
Unit cell |
| |||||||||
Components on special symmetry positions |
| |||||||||
Details | exists as a dodecamer (12) of dimer in solution. This symmetry (x,y,z) shows 3 of 12 active sites per asymmetric unit. Therefore applying the symmetry operators (-x,-y,z), (-x,y,-z), and (x,-y,-z) produces the biological unit. |
-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: 26721.314 Da / Num. of mol.: 3 / Mutation: 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 |
---|
-Non-polymers , 6 types, 1388 molecules
#3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-GOL / #5: Chemical | #6: Chemical | #7: Chemical | ChemComp-BME / #8: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.57 Å3/Da / Density % sol: 52.19 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 1.5-1.8 M ammonium sulfate, 40-60 mM TRIS pH8.5, with 5 mM BME, varying ML:ENZ ratios from 1:2 up to 4:1, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.98 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 9, 2009 / Details: vertical focusing mirror |
Radiation | Monochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.74→50 Å / Num. obs: 145939 / % possible obs: 99.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 5 / Redundancy: 7.2 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 10.3 |
-Phasing
Phasing | Method: molecular replacement |
---|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.74→29.52 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.959 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 1.659 / SU ML: 0.055 / SU R Cruickshank DPI: 0.112 / Cross valid method: THROUGHOUT / ESU R: 0.093 / ESU R Free: 0.089 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 19.5 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.74→29.52 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.741→1.786 Å / Total num. of bins used: 20
|