[English] 日本語
![](img/lk-miru.gif)
- PDB-4qm9: Crystal Structure of a Putative Cysteine Dioxygenase From Bacillu... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 4qm9 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of a Putative Cysteine Dioxygenase From Bacillus subtilis with Cys-bound | ||||||
![]() | Cysteine dioxygenase | ||||||
![]() | OXIDOREDUCTASE / Cupin fold / catalyzes oxidation of cysteine to cysteine sulfinate | ||||||
Function / homology | ![]() cysteine dioxygenase / cysteine dioxygenase activity / L-cysteine catabolic process / oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen / ferrous iron binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hartman, S.H. / Driggers, C.M. / Karplus, P.A. | ||||||
![]() | ![]() Title: Structures of Arg- and Gln-type bacterial cysteine dioxygenase homologs. Authors: Driggers, C.M. / Hartman, S.J. / Karplus, P.A. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 137.1 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 106.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 455.3 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 456.3 KB | Display | |
Data in XML | ![]() | 14 KB | Display | |
Data in CIF | ![]() | 18.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4qm8C ![]() 4qmaC ![]() 3eqeS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 19614.113 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: 168 / Gene: BSU31140, cdoA, Cysteine Dioxygenase, yubC / Plasmid: pET32a / Production host: ![]() ![]() #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.73 Å3/Da / Density % sol: 54.91 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 Details: Purified enzyme was concentrated to 10 mg/mL and 4 uL was mixed with 4 uL of a reservoir containing 18% (w/v) PEG 4000, 0.1 M potassium acetate, 0.05 M MES, pH 6.0, VAPOR DIFFUSION, HANGING ...Details: Purified enzyme was concentrated to 10 mg/mL and 4 uL was mixed with 4 uL of a reservoir containing 18% (w/v) PEG 4000, 0.1 M potassium acetate, 0.05 M MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 12, 2013 |
Radiation | Monochromator: Si(220) Asymmetric cut single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. all: 20271 / Num. obs: 20271 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 23.4 % / Rmerge(I) obs: 0.186 / Rsym value: 0.038 / Net I/σ(I): 13.4 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 13.7 % / Rmerge(I) obs: 2.892 / Mean I/σ(I) obs: 1 / Num. unique all: 1939 / Rsym value: 0.767 / % possible all: 100 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 3eqe Resolution: 2.3→46.66 Å / SU ML: 0.41 / σ(F): 1.33 / Phase error: 29.51 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→46.66 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | S33: -0.0256 Å ° / Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|