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Yorodumi- PDB-1f1x: CRYSTAL STRUCTURE OF HOMOPROTOCATECHUATE 2,3-DIOXYGENASE FROM BRE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1f1x | ||||||
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Title | CRYSTAL STRUCTURE OF HOMOPROTOCATECHUATE 2,3-DIOXYGENASE FROM BREVIBACTERIUM FUSCUM | ||||||
Components | HOMOPROTOCATECHUATE 2,3-DIOXYGENASE | ||||||
Keywords | OXIDOREDUCTASE / Dioxygenase / Extradiol / Iron / Biodegradation / Aromatic | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Brevibacterium fuscum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.6 Å | ||||||
Authors | Vetting, M.W. / Lipscomb, J.D. / Wackett, L.P. / Que Jr., L. / Ohlendorf, D.H. | ||||||
Citation | Journal: J.Bacteriol. / Year: 2004 Title: Crystallographic comparison of manganese- and iron-dependent homoprotocatechuate 2,3-dioxygenases. Authors: Vetting, M.W. / Wackett, L.P. / Que Jr., L. / Lipscomb, J.D. / Ohlendorf, D.H. #1: Journal: J.Biol.Chem. / Year: 1996 Title: Homoprotocatechuate 2,3-dioxygenase from Brevibacterium fuscum. A Dioxygenase with Catalase Activity. Authors: Miller, M.A. / Lipscomb, J.D. #2: Journal: Protein Expr.Purif. / Year: 1997 Title: Cloning, overexpression, and mutagenesis of the gene for homoprotocatechuate 2,3-dioxygenase from Brevibacterium fuscum. Authors: Wang, Y.Z. / 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 | 1f1x.cif.gz | 285.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1f1x.ent.gz | 230 KB | Display | PDB format |
PDBx/mmJSON format | 1f1x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1f1x_validation.pdf.gz | 465 KB | Display | wwPDB validaton report |
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Full document | 1f1x_full_validation.pdf.gz | 475.9 KB | Display | |
Data in XML | 1f1x_validation.xml.gz | 56.2 KB | Display | |
Data in CIF | 1f1x_validation.cif.gz | 83.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f1/1f1x ftp://data.pdbj.org/pub/pdb/validation_reports/f1/1f1x | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological assembly is a tetramer. There is a tetramer per asymmetric unit. |
-Components
#1: Protein | Mass: 37161.516 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Brevibacterium fuscum (bacteria) / Production host: Escherichia coli (E. coli) References: UniProt: Q45135, 3,4-dihydroxyphenylacetate 2,3-dioxygenase #2: Chemical | ChemComp-FEL / #3: 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: 2.52 Å3/Da / Density % sol: 51.12 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: batch crystallization / pH: 7.5 Details: Peg5000, Mg Acetate, MOPS, Glycerol was add prior to data collection., pH 7.5, Batch crystallization, temperature 298K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 200 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.032 |
Detector | Type: CUSTOM-MADE / Detector: CCD / Date: Feb 7, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.032 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→30 Å / Num. all: 234020 / Num. obs: 216266 / % possible obs: 92.4 % / Observed criterion σ(F): 5 / Observed criterion σ(I): 5 / Redundancy: 2.54 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 20 |
Reflection shell | Resolution: 1.5→1.55 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.094 / Num. unique all: 19027 / % possible all: 81.2 |
Reflection | *PLUS Lowest resolution: 20 Å / % possible obs: 92.9 % / Redundancy: 2.55 % / Rmerge(I) obs: 0.041 |
Reflection shell | *PLUS % possible obs: 79.5 % / Redundancy: 1.51 % / Rmerge(I) obs: 0.127 / Mean I/σ(I) obs: 8.7 |
-Processing
Software |
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Refinement | Resolution: 1.6→30 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.6→30 Å
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Refine LS restraints |
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Refinement | *PLUS Lowest resolution: 20 Å / % reflection Rfree: 10 % | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.239 / Rfactor Rwork: 0.187 |