+Open data
-Basic information
Entry | Database: PDB / ID: 2qq5 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of human SDR family member 1 | ||||||
Components | Dehydrogenase/reductase SDR family member 1 | ||||||
Keywords | OXIDOREDUCTASE / DHRS1 / SDR / DEHYDROGENASE / REDUCTASE / SHORT-CHAIN / STRUCTURAL GENOMICS CONSORTIUM / SGC | ||||||
Function / homology | Function and homology information Oxidoreductases; Acting on the CH-OH group of donors / oxidoreductase activity / endoplasmic reticulum Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Pilka, E.S. / Hozjan, V. / Ugochukwu, E. / von Delft, F. / Sundstrom, M. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / Oppermann, U. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: TO BE PUBLISHED Title: Crystal structure of human SDR family member 1. Authors: Pilka, E.S. / Hozjan, V. / Ugochukwu, E. / von Delft, F. / Sundstrom, M. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / Oppermann, U. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2qq5.cif.gz | 61.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2qq5.ent.gz | 44 KB | Display | PDB format |
PDBx/mmJSON format | 2qq5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qq/2qq5 ftp://data.pdbj.org/pub/pdb/validation_reports/qq/2qq5 | HTTPS FTP |
---|
-Related structure data
Related structure data | 1ae1S 1ahhS 1vl8S 1zemS 2ae1S 2ew8S S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 28044.129 Da / Num. of mol.: 1 / Fragment: Residues 3-262 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DHRS1 / Plasmid: p11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3 References: UniProt: Q96LJ7, Oxidoreductases; Acting on the CH-OH group of donors |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.46 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 2.4M Na Malonate pH 7.0, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Jul 5, 2007 / Details: OSMIC |
Radiation | Monochromator: OSMIC / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→22.21 Å / Num. all: 91682 / Num. obs: 91499 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Rmerge(I) obs: 0.056 / Rsym value: 0.065 / Net I/σ(I): 17.8 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.567 / Mean I/σ(I) obs: 2 / Num. unique all: 12938 / Rsym value: 0.66 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entries 2AE1, 1AE1, 2EW8, 1ZEM, 1AHH, 1VL8 Resolution: 1.8→22.21 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.945 / SU B: 4.406 / SU ML: 0.07 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.106 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: The Friedel pairs were used for phasing. 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 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.684 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→22.21 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: 20.6303 Å / Origin y: 29.9874 Å / Origin z: 34.7302 Å
|