[English] 日本語
Yorodumi- PDB-2ig9: Structure of a full-length Homoprotocatechuate 2,3-Dioxygenase fr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ig9 | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of a full-length Homoprotocatechuate 2,3-Dioxygenase from B. fuscum in a new spacegroup. | ||||||
Components | Homoprotocatechuate 2,3-dioxygenase | ||||||
Keywords | OXIDOREDUCTASE / oxygenase / extradiol / Fe(II) / homoprotocatechuate | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Brevibacterium fuscum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2ig9.cif.gz | 325.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2ig9.ent.gz | 262.7 KB | Display | PDB format |
PDBx/mmJSON format | 2ig9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ig/2ig9 ftp://data.pdbj.org/pub/pdb/validation_reports/ig/2ig9 | HTTPS FTP |
---|
-Related structure data
Related structure data | 2igaC 1f1xS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
| ||||||||
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 |
---|
-Non-polymers , 5 types, 1268 molecules
#2: Chemical | ChemComp-FE2 / #3: Chemical | ChemComp-CL / #4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-CA / | #6: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 45.92 % |
---|---|
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. 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 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.23983 Å |
Detector | Type: NOIR-1 / Detector: CCD / Date: Apr 24, 2005 |
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: 1.9→53.15 Å / Num. all: 133141 / Num. obs: 132886 / % possible obs: 99.8 % / Redundancy: 3.18 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 7.1 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.532 / Mean I/σ(I) obs: 2 / Num. unique all: 13150 / % possible all: 99.9 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1F1X Resolution: 1.9→46.08 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.933 / SU B: 4.197 / SU ML: 0.118 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.153 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: Full length enzyme structure solved by molecular replacement using truncated 1F1X (PDB code) structure.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 23.337 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→46.08 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20
|