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Yorodumi- PDB-3bza: Structure of Mn-substituted Homoprotocatechuate 2,3-Dioxygenase f... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3bza | ||||||
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Title | Structure of Mn-substituted Homoprotocatechuate 2,3-Dioxygenase from B.fuscum at 1.7 Ang resolution | ||||||
Components | Homoprotocatechuate 2,3-dioxygenase | ||||||
Keywords | OXIDOREDUCTASE / oxygenase / extradiol / Mn II / metal substitution / Dioxygenase | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Brevibacterium fuscum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Kovaleva, E.G. / Lipscomb, J.D. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.Usa / Year: 2008 Title: Swapping metals in Fe- and Mn-dependent dioxygenases: evidence for oxygen activation without a change in metal redox state. Authors: Emerson, J.P. / Kovaleva, E.G. / Farquhar, E.R. / Lipscomb, J.D. / Que, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3bza.cif.gz | 324.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3bza.ent.gz | 259.7 KB | Display | PDB format |
PDBx/mmJSON format | 3bza.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bz/3bza ftp://data.pdbj.org/pub/pdb/validation_reports/bz/3bza | HTTPS FTP |
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-Related structure data
Related structure data | 2ig9S 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 | Asymmetric unit containing a single tetramer (chains A,B,C,D) represents biologically active 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 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 References: UniProt: Q45135, 3,4-dihydroxyphenylacetate 2,3-dioxygenase |
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-Non-polymers , 5 types, 1259 molecules
#2: Chemical | ChemComp-MN / #3: Chemical | ChemComp-CL / #4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-CA / | #6: 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: 2.42 Å3/Da / Density % sol: 49.25 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 18% PEG8000, 0.2 M calcium acetate, 0.1 M sodium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97857 Å |
Detector | Type: SBC-3 / Detector: CCD / Date: Oct 13, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→55 Å / Num. obs: 167766 / % possible obs: 99.3 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.088 / Rsym value: 0.088 / Net I/σ(I): 15.308 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.555 / Mean I/σ(I) obs: 2.258 / Num. unique all: 17278 / % possible all: 98.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2IG9 Resolution: 1.7→28.82 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.943 / SU B: 1.926 / SU ML: 0.064 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.1 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.204 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→28.82 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.701→1.745 Å / Total num. of bins used: 20
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