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Yorodumi- PDB-2iga: Structure of Homoprotocatechuate 2,3-Dioxygenase from B. fuscum i... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2iga | ||||||
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Title | Structure of Homoprotocatechuate 2,3-Dioxygenase from B. fuscum in complex with reactive intermediates formed via in crystallo reaction with 4-nitrocatechol at low oxygen concentrations. | ||||||
Components | Homoprotocatechuate 2,3-dioxygenase | ||||||
Keywords | OXIDOREDUCTASE / oxygenase / extradiol / Fe(II) / homoprotocatechuate / alkylperoxo intermediate / substrate-semiquinone / open-ring product | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Brevibacterium fuscum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Kovaleva, E.G. / Lipscomb, J.D. | ||||||
Citation | Journal: Science / Year: 2007 Title: Crystal structures of Fe2+ dioxygenase superoxo, alkylperoxo, and bound product intermediates Authors: Kovaleva, E.G. / 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 | 2iga.cif.gz | 325.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2iga.ent.gz | 261.5 KB | Display | PDB format |
PDBx/mmJSON format | 2iga.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2iga_validation.pdf.gz | 518.6 KB | Display | wwPDB validaton report |
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Full document | 2iga_full_validation.pdf.gz | 535 KB | Display | |
Data in XML | 2iga_validation.xml.gz | 64 KB | Display | |
Data in CIF | 2iga_validation.cif.gz | 92.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ig/2iga ftp://data.pdbj.org/pub/pdb/validation_reports/ig/2iga | HTTPS FTP |
-Related structure data
Related structure data | 2ig9C 1f1xS 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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Components on special symmetry positions |
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Details | A homotetramer composed of chains A-D is the biological unit |
-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 41755.320 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Brevibacterium fuscum (bacteria) / Strain: ATCC 15993 / Gene: hpcd / Plasmid: pYZW204 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: Q45135, 3,4-dihydroxyphenylacetate 2,3-dioxygenase |
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-Non-polymers , 9 types, 1069 molecules
#2: Chemical | ChemComp-FE2 / #3: Chemical | ChemComp-CL / #4: Chemical | ChemComp-XXP / | #5: Chemical | ChemComp-GOL / #6: Chemical | ChemComp-CA / | #7: Chemical | #8: Chemical | ChemComp-XX2 / | #9: Chemical | ChemComp-OXY / | #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: 2.25 Å3/Da / Density % sol: 45.01 % |
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Crystal grow | Temperature: 292 K / pH: 6.5 Details: 18% PEG8000, 0.2 M calcium acetate, 0.1 M sodium cacodylate. Prior to freezing in liquid nitrogen, crystals were sequentially transferred into mother liquor solutions containing 5, 10, 15, ...Details: 18% PEG8000, 0.2 M calcium acetate, 0.1 M sodium cacodylate. Prior to freezing in liquid nitrogen, crystals were sequentially transferred into mother liquor solutions containing 5, 10, 15, and then 20% glycerol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K, pH 6.50 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.23983 |
Detector | Type: NOIR-1 / Detector: CCD / Date: May 20, 2006 |
Radiation | Monochromator: ROSENBAUM-ROCK SAGITALLY FOCUSED SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.23983 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→52.7 Å / Num. obs: 105058 / % possible obs: 87.8 % / Redundancy: 2.08 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 5.4 |
Reflection shell | Resolution: 1.95→2.02 Å / Redundancy: 2.16 % / Rmerge(I) obs: 0.379 / Mean I/σ(I) obs: 1.9 / % possible all: 91.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1F1X Resolution: 1.95→52.7 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.929 / SU B: 4.316 / SU ML: 0.123 / Isotropic thermal model: isotropic / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.59 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→52.7 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2 Å
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