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- PDB-3vzy: Crystal structure of PcrB complexed with G1P from bacillus subtil... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3vzy | ||||||
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Title | Crystal structure of PcrB complexed with G1P from bacillus subtilis subap. subtilis str. 168 | ||||||
![]() | Heptaprenylglyceryl phosphate synthase | ||||||
![]() | TRANSFERASE / biosynthesis / prenyltransferases / enzyme catalysis | ||||||
Function / homology | ![]() : / glycerophospholipid biosynthetic process / polyprenyltransferase activity / magnesium ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | 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. | ||||||
![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 115.4 KB | Display | ![]() |
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PDB format | ![]() | 87 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 457.7 KB | Display | ![]() |
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Full document | ![]() | 463 KB | Display | |
Data in XML | ![]() | 24.5 KB | Display | |
Data in CIF | ![]() | 36.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3vzxSC ![]() 3vzzC ![]() 3w00C ![]() 3w01C ![]() 3w02C S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 25110.629 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: O34790, Transferases; Transferring alkyl or aryl groups, other than methyl groups #2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-CL / #4: Chemical | ChemComp-1GP / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.48 % |
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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 |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 17, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.63→50 Å / Num. obs: 52267 / % possible obs: 96.9 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 23.3 |
Reflection shell | Resolution: 1.63→1.69 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.285 / Mean I/σ(I) obs: 3.7 / Num. unique all: 4962 / % possible all: 92.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3VZX Resolution: 1.63→25.89 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.63→25.89 Å
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LS refinement shell | Resolution: 1.63→1.69 Å
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