[English] 日本語
Yorodumi- PDB-3ojk: Structure of Co-substituted Homoprotocatechuate 2,3-Dioxygenase i... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ojk | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of Co-substituted Homoprotocatechuate 2,3-Dioxygenase in complex with 4-nitrocatechol at 1.68 Ang resolution | ||||||
Components | Homoprotocatechuate 2,3-dioxygenase | ||||||
Keywords | OXIDOREDUCTASE / dioxygenase / extradiol / metal substitution / 4-nitrocatechol / 2-His-1-carboxylate facial triad / aromatic ring cleavage | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Brevibacterium fuscum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 Å | ||||||
Authors | Fielding, A.J. / Kovaleva, E.G. / Farquhar, E.R. / Lipscomb, J.D. / Que Jr., L. | ||||||
Citation | Journal: J.Biol.Inorg.Chem. / Year: 2011 Title: A hyperactive cobalt-substituted extradiol-cleaving catechol dioxygenase. Authors: Fielding, A.J. / Kovaleva, E.G. / Farquhar, E.R. / Lipscomb, J.D. / Que, L. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3ojk.cif.gz | 606.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3ojk.ent.gz | 501.6 KB | Display | PDB format |
PDBx/mmJSON format | 3ojk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oj/3ojk ftp://data.pdbj.org/pub/pdb/validation_reports/oj/3ojk | HTTPS FTP |
---|
-Related structure data
Related structure data | 3ojjC 3ojnC 3ojtC 2ig9S 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 |
|
-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 |
---|
-Non-polymers , 7 types, 1389 molecules
#2: Chemical | ChemComp-CO / #3: Chemical | #4: Chemical | ChemComp-CL / #5: Chemical | ChemComp-P6G / #6: Chemical | ChemComp-CA / | #7: Chemical | #8: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.27 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 13% PEG6000, 0.1 M calcium chloride, 0.1 M Tris-HCl. Cryoprotectant 25% PEG400, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9801 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 21, 2010 |
Radiation | Monochromator: Channel cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9801 Å / Relative weight: 1 |
Reflection | Resolution: 1.68→41.19 Å / Num. all: 180226 / Num. obs: 175180 / % possible obs: 97.2 % / Observed criterion σ(I): 3 / Redundancy: 5.8 % / Biso Wilson estimate: 18.8 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 1.68→1.77 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.346 / Mean I/σ(I) obs: 2.1 / Num. unique all: 23848 / Rsym value: 0.742 / % possible all: 91.7 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2IG9 Resolution: 1.68→37.96 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.958 / SU B: 4.068 / SU ML: 0.062 / Cross valid method: THROUGHOUT / ESU R: 0.091 / ESU R Free: 0.089 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 20.873 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.68→37.96 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.68→1.724 Å / Total num. of bins used: 20
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|