[English] 日本語
Yorodumi- PDB-3db2: Crystal structure of a putative nadph-dependent oxidoreductase (d... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3db2 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of a putative nadph-dependent oxidoreductase (dhaf_2064) from desulfitobacterium hafniense dcb-2 at 1.70 A resolution | ||||||
Components | putative NADPH-dependent oxidoreductase | ||||||
Keywords | OXIDOREDUCTASE / Two domain protein / rossmann fold / putative dehydrogenase / structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Desulfitobacterium hafniense DCB-2 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: To be published Title: Crystal structure of putative NADPH-dependent oxidoreductase (ZP_01370612.1) from DESULFITOBACTERIUM HAFNIENSE DCB-2 at 1.70 A resolution Authors: Joint Center for Structural Genomics (JCSG) | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3db2.cif.gz | 221.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3db2.ent.gz | 179.7 KB | Display | PDB format |
PDBx/mmJSON format | 3db2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/db/3db2 ftp://data.pdbj.org/pub/pdb/validation_reports/db/3db2 | HTTPS FTP |
---|
-Related structure data
Similar structure data | |
---|---|
Other databases |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
| ||||||||
Details | AUTHORS STATE THAT SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIZATION STATE. |
-Components
#1: Protein | Mass: 39909.992 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Desulfitobacterium hafniense DCB-2 (bacteria) Gene: ZP_01370612.1, Dhaf_4026 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q18XG3, UniProt: B8FRW3*PLUS #2: Chemical | #3: Water | ChemComp-HOH / | Sequence details | THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATI | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
---|
-Sample preparation
Crystal |
| |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow |
|
-Data collection
Diffraction |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Single crystal Si(111) bent monochromator (horizontal focusing) Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.7→29.748 Å / Num. obs: 120878 / % possible obs: 99.9 % / Redundancy: 9.9 % / Rmerge(I) obs: 0.1 / Rsym value: 0.1 / Net I/σ(I): 4.6 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 2
|
-Phasing
Phasing | Method: MAD |
---|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MAD / Resolution: 1.7→29.748 Å / Num. parameters: 34792 / Num. restraintsaints: 62193 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. GLYCEROL MOLECULES FROM THE CRYSTALLIZATION SOLUTION ARE MODELED. 4. THE DIFFRACTION DATA IS TWINNED WITH THE TWINNING OPERATOR "-H,-K,L" AND THE REFINED TWIN FRACTION IS 0.407.
| ||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228 | ||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.353 Å2 | ||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→29.748 Å
| ||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|