[English] 日本語
Yorodumi- PDB-6cng: The X-ray crystal structure of the Streptococcus pneumoniae Fatty... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6cng | ||||||
---|---|---|---|---|---|---|---|
Title | The X-ray crystal structure of the Streptococcus pneumoniae Fatty Acid Kinase (Fak) B3 protein loaded with linoleic acid to 1.47 Angstrom resolution | ||||||
Components | Fatty Acid Kinase (Fak) B3 protein | ||||||
Keywords | TRANSFERASE / Streptococcus pneumoniae / Fatty acid kinase / Linoleic acid | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptococcus pneumoniae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 Å | ||||||
Authors | Cuypers, M.G. / Subramanian, C. / White, S.W. / Rock, C.O. | ||||||
Funding support | United States, 1items
| ||||||
Citation | Journal: To Be Published Title: The X-ray crystal structure of the Streptococcus pneumoniae Fatty Acid Kinase (Fak) B3 protein loaded with linoleic acid to 1.47 Angstrom resolution Authors: Cuypers, M.G. / Subramanian, C. / White, S.W. / Rock, C.O. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6cng.cif.gz | 360.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6cng.ent.gz | 296.5 KB | Display | PDB format |
PDBx/mmJSON format | 6cng.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6cng_validation.pdf.gz | 836.7 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6cng_full_validation.pdf.gz | 846.2 KB | Display | |
Data in XML | 6cng_validation.xml.gz | 32 KB | Display | |
Data in CIF | 6cng_validation.cif.gz | 49.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cn/6cng ftp://data.pdbj.org/pub/pdb/validation_reports/cn/6cng | HTTPS FTP |
-Related structure data
Related structure data | 3fdjS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 2 molecules AD
#1: Protein | Mass: 32866.352 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pneumoniae (strain ATCC BAA-255 / R6) (bacteria) Strain: ATCC BAA-255 / R6 / Gene: spr0652 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8DQI6 |
---|
-Non-polymers , 5 types, 817 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-ACT / #6: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 52.4 % / Description: prismatic |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 0.1M Na acetate pH 4.6, 8% PEG 4000. Cryofreezing solution soak in motherliquor with 25% glycerol Temp details: controlled temperature room |
-Data collection
Diffraction | Mean temperature: 100 K Ambient temp details: on cryostream (from Liq N2 flashfreeze) |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Oct 15, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.47→62.11 Å / Num. obs: 108472 / % possible obs: 96.2 % / Redundancy: 3 % / Biso Wilson estimate: 17.283 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.036 / Rpim(I) all: 0.025 / Rrim(I) all: 0.044 / Net I/σ(I): 15 |
Reflection shell | Resolution: 1.47→1.5 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.544 / Num. unique obs: 5188 / CC1/2: 0.574 / Rpim(I) all: 0.386 / Rrim(I) all: 0.669 / % possible all: 94.1 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3fdj (modified with MODBASE server) Resolution: 1.47→43.972 Å / Cross valid method: FREE R-VALUE / σ(F): 6.03 / Phase error: 19.34 / Details: H atoms are isotropic, not H atoms are anisotropic
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.47→43.972 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: 4.88 Å / Origin y: -6.4633 Å / Origin z: -0.3321 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Selection details: all |