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Yorodumi- PDB-4ghd: Structure of Y257F variant of Homoprotocatechuate 2,3-Dioxygenase... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ghd | ||||||
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Title | Structure of Y257F variant of Homoprotocatechuate 2,3-Dioxygenase from B.fuscum in complex with HPCA at 1.85 Ang resolution | ||||||
Components | Homoprotocatechuate 2,3-dioxygenase | ||||||
Keywords | OXIDOREDUCTASE / Dioxygenase / oxygen activation / Fe(II) / 2-His-1-carboxylate facial triad / homoprotocatechuate / 4-nitrocatechol / oxy complex | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Brevibacterium fuscum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Kovaleva, E.G. / Lipscomb, J.D. | ||||||
Citation | Journal: Biochemistry / Year: 2012 Title: Structural basis for the role of tyrosine 257 of homoprotocatechuate 2,3-dioxygenase in substrate and oxygen activation. 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 | 4ghd.cif.gz | 604.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ghd.ent.gz | 499.6 KB | Display | PDB format |
PDBx/mmJSON format | 4ghd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gh/4ghd ftp://data.pdbj.org/pub/pdb/validation_reports/gh/4ghd | HTTPS FTP |
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-Related structure data
Related structure data | 4ghcC 4gheC 4ghfC 4ghgC 4ghhC 3ojtS 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
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 41739.320 Da / Num. of mol.: 4 / Mutation: Y257F 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 , 7 types, 1222 molecules
#2: Chemical | ChemComp-FE2 / #3: Chemical | ChemComp-P6G / #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-CA / | #7: Chemical | ChemComp-DHY / | #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: 2.39 Å3/Da / Density % sol: 48.52 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 13% PEG6000, 0.1M calcium chloride, 0.1M Tris-HCl. Cryoprotectant 25% PEG400. Ligand soaking: 2mM HPCA for 3 hours in anaerobic glovebox atmosphere prior to cryo-cooling in liquid nitrogen., ...Details: 13% PEG6000, 0.1M calcium chloride, 0.1M Tris-HCl. Cryoprotectant 25% PEG400. Ligand soaking: 2mM HPCA for 3 hours in anaerobic glovebox atmosphere prior to cryo-cooling in liquid nitrogen., pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9801 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 21, 2011 Details: Kirkpatrick-Baez pair of bi-morph mirrors plus channel cut cryogenically cooled monochromator crystal |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9801 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→48.1 Å / Num. all: 134568 / Num. obs: 134568 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.9 % / Rmerge(I) obs: 0.045 / Net I/σ(I): 13.4 |
Reflection shell | Resolution: 1.85→1.95 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.424 / Mean I/σ(I) obs: 1.9 / Num. unique all: 19149 / % possible all: 97.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3OJT Resolution: 1.85→48.05 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.953 / SU B: 5.194 / SU ML: 0.08 / Cross valid method: THROUGHOUT / ESU R: 0.121 / ESU R Free: 0.115 / 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: 27.973 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→48.05 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.898 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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