[English] 日本語
![](img/lk-miru.gif)
- PDB-6wfh: Streptomyces coelicolor methylmalonyl-CoA epimerase substrate complex -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 6wfh | ||||||
---|---|---|---|---|---|---|---|
Title | Streptomyces coelicolor methylmalonyl-CoA epimerase substrate complex | ||||||
![]() | Methylmalonyl-CoA epimerase | ||||||
![]() | ISOMERASE / Epimerase / acid-base / enol / enolate | ||||||
Function / homology | ![]() methylmalonyl-CoA epimerase activity / L-methylmalonyl-CoA metabolic process / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Stunkard, L.M. / Benjamin, A.B. / Bower, J.B. / Huth, T.J. / Lohman, J.R. | ||||||
![]() | ![]() Title: Substrate Enolate Intermediate and Mimic Captured in the Active Site of Streptomyces coelicolor Methylmalonyl-CoA Epimerase. Authors: Stunkard, L.M. / Benjamin, A.B. / Bower, J.B. / Huth, T.J. / Lohman, J.R. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 51 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 32 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 6wf6C ![]() 6wf7C ![]() 6wfiC ![]() 1jc5S S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| |||||||||
Unit cell |
| |||||||||
Components on special symmetry positions |
|
-
Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 16059.767 Da / Num. of mol.: 1 / Mutation: M1S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
---|
-Non-polymers , 6 types, 121 molecules ![](data/chem/img/CO.gif)
![](data/chem/img/V0V.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/V0V.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-CO / | ||||
---|---|---|---|---|---|
#3: Chemical | ChemComp-V0V / ( | ||||
#4: Chemical | ChemComp-SO4 / | ||||
#5: Chemical | #6: Chemical | ChemComp-CL / | #7: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.67 Å3/Da / Density % sol: 66.54 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 25 mM sodium chloride, 100 mM Bis-Tris:HCl pH 7.0, 2.7 M ammonium sulfate, 5% PEG 400 |
-Data collection
Diffraction | Mean temperature: 80 K / Ambient temp details: liquid nitrogen / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Feb 23, 2020 / Details: MD2 Micro Diffractometer |
Diffraction measurement | Details: 1.00 degrees, -1.0 sec, detector distance 199.45 mm Method: \w scans |
Radiation | Monochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Av R equivalents: 0.12 / Number: 288418 |
Reflection | Resolution: 1.84→30 Å / Num. obs: 21795 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 13.2 % / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.035 / Rrim(I) all: 0.126 / Rsym value: 0.12 / Χ2: 0.999 / Net I/av σ(I): 18.968 / Net I/σ(I): 9 |
Reflection shell | Resolution: 1.85→1.92 Å / Redundancy: 13.5 % / Rmerge(I) obs: 1.103 / Mean I/σ(I) obs: 2.632 / Num. unique obs: 2123 / Rsym value: 1.103 / % possible all: 100 |
Cell measurement | Reflection used: 288418 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 1JC5 Resolution: 1.84→29.31 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.971 / WRfactor Rfree: 0.2153 / WRfactor Rwork: 0.1832 / FOM work R set: 0.8702 / SU B: 2.108 / SU ML: 0.062 / SU R Cruickshank DPI: 0.088 / SU Rfree: 0.0866 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.088 / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 max: 107.82 Å2 / Biso mean: 37.613 Å2 / Biso min: 26.15 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.84→29.31 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.842→1.89 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
|