[English] 日本語
Yorodumi- PDB-3w00: Crystal structure of PcrB complexed with G1P and FsPP from bacill... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3w00 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of PcrB complexed with G1P and FsPP from bacillus subtilis subap. subtilis str. 168 | ||||||
Components | Heptaprenylglyceryl phosphate synthase | ||||||
Keywords | TRANSFERASE / biosynthesis / prenyltransferases / enzyme catalysis | ||||||
Function / homology | Function and homology information : / glycerophospholipid biosynthetic process / polyprenyltransferase activity / magnesium ion binding Similarity search - Function | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Ren, F. / Feng, X. / Ko, T.P. / Huang, C.H. / Hu, Y. / Chan, H.C. / Liu, Y.L. / Wang, K. / Chen, C.C. / Pang, X. ...Ren, F. / Feng, X. / Ko, T.P. / Huang, C.H. / Hu, Y. / Chan, H.C. / Liu, Y.L. / Wang, K. / Chen, C.C. / Pang, X. / He, M. / Li, Y. / Oldfield, E. / Guo, R.T. | ||||||
Citation | Journal: Chembiochem / Year: 2013 Title: Insights into TIM-barrel prenyl transferase mechanisms: crystal structures of PcrB from Bacillus subtilis and Staphylococcus aureus Authors: Ren, F. / Feng, X. / Ko, T.P. / Huang, C.H. / Hu, Y. / Chan, H.C. / Liu, Y.L. / Wang, K. / Chen, C.C. / Pang, X. / He, M. / Li, Y. / Oldfield, E. / Guo, R.T. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3w00.cif.gz | 102.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3w00.ent.gz | 78.5 KB | Display | PDB format |
PDBx/mmJSON format | 3w00.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3w00_validation.pdf.gz | 652.9 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3w00_full_validation.pdf.gz | 664.7 KB | Display | |
Data in XML | 3w00_validation.xml.gz | 21.4 KB | Display | |
Data in CIF | 3w00_validation.cif.gz | 29.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w0/3w00 ftp://data.pdbj.org/pub/pdb/validation_reports/w0/3w00 | HTTPS FTP |
-Related structure data
Related structure data | 3vzxSC 3vzyC 3vzzC 3w01C 3w02C S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 25110.629 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: pcrB / Plasmid: pET32a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) References: UniProt: O34790, Transferases; Transferring alkyl or aryl groups, other than methyl groups #2: Chemical | ChemComp-PO4 / | #3: Chemical | ChemComp-FPS / | #4: Chemical | ChemComp-1GP / | #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45.2 % |
---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 2.5M NaCl, 14% PEG6000, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 30, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→25 Å / Num. obs: 15342 / % possible obs: 98.6 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 16.1 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 2.7 / Num. unique all: 1440 / % possible all: 92.8 |
-Processing
Software |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3vZX Resolution: 2.5→24.61 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→24.61 Å
| ||||||||||||||||||||
LS refinement shell | Resolution: 2.5→2.59 Å /
|