[English] 日本語
Yorodumi- PDB-2opw: Crystal structure of human phytanoyl-CoA dioxygenase PHYHD1 (apo) -
+Open data
-Basic information
Entry | Database: PDB / ID: 2opw | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of human phytanoyl-CoA dioxygenase PHYHD1 (apo) | ||||||
Components | PHYHD1 protein | ||||||
Keywords | OXIDOREDUCTASE / PHYHD1 / double-stranded beta helix / oxygenase / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
Function / homology | Function and homology information Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor / 2-oxoglutarate-dependent dioxygenase activity / Oxidoreductases / dioxygenase activity / metal ion binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Zhang, Z. / Butler, D. / McDonough, M.A. / Kavanagh, K.L. / Bray, J.E. / Ng, S.S. / von Delft, F. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. ...Zhang, Z. / Butler, D. / McDonough, M.A. / Kavanagh, K.L. / Bray, J.E. / Ng, S.S. / von Delft, F. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / Sundstrom, M. / Schofield, C.J. / Oppermann, U. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: To be Published Title: Crystal structure of human phytanoyl-CoA dioxygenase PHYHD1 (apo) Authors: Zhang, Z. / Butler, D. / McDonough, M.A. / Kavanagh, K.L. / Bray, J.E. / Ng, S.S. / von Delft, F. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / Sundstrom, M. / Schofield, C.J. / Oppermann, U. | ||||||
History |
| ||||||
Remark 300 | BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). AUTHORS STATE THAT THE DISULFIDE BOND FORMED BETWEEN CRYSTALLOGRAPHICALLY RELATED MONOMERS VIA CYS3 IS PROBABLY NOT BIOLOGICALLY RELEVANT. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2opw.cif.gz | 70.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2opw.ent.gz | 52.5 KB | Display | PDB format |
PDBx/mmJSON format | 2opw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/op/2opw ftp://data.pdbj.org/pub/pdb/validation_reports/op/2opw | HTTPS FTP |
---|
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 32445.768 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Tissue: Lung / Gene: PHYHD1 / Plasmid: pET / Production host: Escherichia coli (E. coli) References: UniProt: Q7Z623, UniProt: Q5SRE7*PLUS, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation ...References: UniProt: Q7Z623, UniProt: Q5SRE7*PLUS, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.07 Å3/Da / Density % sol: 59.92 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 7% PEG3350, 200mM Calcium acetate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9552 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 1, 2006 |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9552 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→40.06 Å / Num. all: 31832 / Num. obs: 31832 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Biso Wilson estimate: 22 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 10 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 6 % / Mean I/σ(I) obs: 2.24 / % possible all: 92.5 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Model built from sulfur SAD data Resolution: 1.9→40.06 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.941 / SU B: 12.522 / SU ML: 0.161 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.143 / ESU R Free: 0.14 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Extra density near SER 198 could not be identified and was left unmodelled
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.811 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→40.06 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.9→1.95 Å / Total num. of bins used: 20
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: 29.1035 Å / Origin y: -30.7782 Å / Origin z: -4.3326 Å
|