[English] 日本語
Yorodumi- PDB-6s6f: Crystal structure of 2-methylcitrate synthase (PrpC) from Pseudom... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6s6f | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of 2-methylcitrate synthase (PrpC) from Pseudomonas aeruginosa in apo form. | |||||||||
Components | Citrate synthase | |||||||||
Keywords | TRANSFERASE / 2-methlycitrate synthase / PrpC / propionate metabolism / methylcitrate cycle | |||||||||
Function / homology | Function and homology information 2-methylcitrate synthase activity / propionate metabolic process, methylcitrate cycle / citrate synthase activity / tricarboxylic acid cycle heteromeric enzyme complex / citrate (Si)-synthase activity / tricarboxylic acid cycle / carbohydrate metabolic process Similarity search - Function | |||||||||
Biological species | Pseudomonas aeruginosa PAO1 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 Å | |||||||||
Authors | Wijaya, A.J. / Brear, P. / Dolan, S.K. / Welch, M. | |||||||||
Funding support | United Kingdom, 2items
| |||||||||
Citation | Journal: To Be Published Title: Crystal structure of 2-methylcitrate synthase (PrpC) from Pseudomonas aeruginosa in apo form. Authors: Wijaya, A.J. / Brear, P. / Dolan, S.K. / Welch, M. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6s6f.cif.gz | 159.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6s6f.ent.gz | 125.1 KB | Display | PDB format |
PDBx/mmJSON format | 6s6f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6s6f_validation.pdf.gz | 306.4 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6s6f_full_validation.pdf.gz | 310.1 KB | Display | |
Data in XML | 6s6f_validation.xml.gz | 27.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s6/6s6f ftp://data.pdbj.org/pub/pdb/validation_reports/s6/6s6f | HTTPS FTP |
-Related structure data
Related structure data | 3tqgS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 41741.473 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: prpC, PA0795 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9I5E3 #2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-CL / | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.64 % |
---|---|
Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop Details: 100 mM Bis-Tris pH 5.5, 15-25% PEG3350, 40 mM D-Xylose |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å | |||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 28, 2017 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 1.53→57.99 Å / Num. obs: 101668 / % possible obs: 99.9 % / Redundancy: 3.2 % / Biso Wilson estimate: 19.11 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.036 / Rrim(I) all: 0.067 / Net I/σ(I): 8.9 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3TQG Resolution: 1.53→57.99 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 25.85
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 96.56 Å2 / Biso mean: 26.3302 Å2 / Biso min: 10.89 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.53→57.99 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
|