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Yorodumi- PDB-3mv4: Axial Ligand Swapping In Double Mutant Maintains Intradiol-cleava... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3mv4 | ||||||
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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 / intradiol / non-heme / holoenzyme / ferric iron | ||||||
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: 1.59 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 | 3mv4.cif.gz | 318.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3mv4.ent.gz | 255.3 KB | Display | PDB format |
PDBx/mmJSON format | 3mv4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3mv4_validation.pdf.gz | 535 KB | Display | wwPDB validaton report |
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Full document | 3mv4_full_validation.pdf.gz | 550.8 KB | Display | |
Data in XML | 3mv4_validation.xml.gz | 69.1 KB | Display | |
Data in CIF | 3mv4_validation.cif.gz | 100.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mv/3mv4 ftp://data.pdbj.org/pub/pdb/validation_reports/mv/3mv4 | HTTPS FTP |
-Related structure data
Related structure data | 3mflC 3mi1C 3mi5C 3mv6C 3t63C 3t67C 2pcdS C: citing same article (ref.) S: Starting model for refinement |
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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 | The alpha-beta subunits make one monomer (of two chains). There are 12 monomers (dodecamer) in the biological assembly. Applying the symmetry operations (-x,-y,z), (-x,y,-z), and (x,-y,-z) to (x,y,z) yields one 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, pcaH / Plasmid: pCE025 / 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: pCE025 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) References: UniProt: P00437, protocatechuate 3,4-dioxygenase |
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-Non-polymers , 6 types, 1634 molecules A
#3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-BME / #6: Chemical | #7: Chemical | ChemComp-CO3 / #8: 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: 52.28 % |
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Crystal grow | Temperature: 277 K / pH: 8.5 Details: 1.5-1.8 M ammonium sulfate, 2-5 mM beta-mercaptoethanol, and 40-60 mM TRIS-HCl pH 8.5 , 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: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 15, 2009 / Details: MIRRORS |
Radiation | Monochromator: SAGITALLY FOCUSED DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.59→50 Å / Num. obs: 199921 / % possible obs: 99.5 % / Observed criterion σ(I): 3 / Redundancy: 5.4 % / Biso Wilson estimate: 17.4 Å2 / Rmerge(I) obs: 0.043 / Net I/σ(I): 20.7 |
Reflection shell | Resolution: 1.59→1.62 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.291 / Mean I/σ(I) obs: 4.6 / % possible all: 97.2 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: A TRUNCATED MODEL MADE FROM PDB ID = 2PCD Resolution: 1.59→30.6 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.965 / Occupancy max: 1 / Occupancy min: 0 / SU B: 1.164 / SU ML: 0.042 / SU R Cruickshank DPI: 0.072 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R Free: 0.07 / 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: 19.98 Å2
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Refinement step | Cycle: LAST / Resolution: 1.59→30.6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.59→1.63 Å / Total num. of bins used: 20
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