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Yorodumi- PDB-3we9: The crystal structure of YisP from Bacillus subtilis subsp. subti... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3we9 | ||||||
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Title | The crystal structure of YisP from Bacillus subtilis subsp. subtilis strain 168 | ||||||
Components | Putative phytoene/squalene synthase YisP | ||||||
Keywords | TRANSFERASE / Bacillus subtilis YisP / Isoprenoid / Biofilm / DXXXD motif / squalene synthase | ||||||
Function / homology | Function and homology information farnesyl diphosphatase / geranylgeranyl-diphosphate geranylgeranyltransferase activity / isoprenoid biosynthetic process / hydrolase activity Similarity search - Function | ||||||
Biological species | Bacillus subtilis subsp. subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.92 Å | ||||||
Authors | Hu, Y. / Huang, C.H. / Chan, H.C. / Ko, T.P. / Feng, X. / Oldfield, E. / Guo, R.T. | ||||||
Citation | Journal: To be Published Title: Crystal structure of Bacillus subtilis YisP in complex with a PEG fragment Authors: Hu, Y. / Huang, C.H. / Chan, H.C. / Ko, T.P. / Feng, X. / Oldfield, E. / Guo, R.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3we9.cif.gz | 66 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3we9.ent.gz | 49 KB | Display | PDB format |
PDBx/mmJSON format | 3we9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3we9_validation.pdf.gz | 438.9 KB | Display | wwPDB validaton report |
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Full document | 3we9_full_validation.pdf.gz | 442.7 KB | Display | |
Data in XML | 3we9_validation.xml.gz | 14.3 KB | Display | |
Data in CIF | 3we9_validation.cif.gz | 20.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/we/3we9 ftp://data.pdbj.org/pub/pdb/validation_reports/we/3we9 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 31546.045 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis subsp. subtilis (bacteria) Strain: 168 / Gene: yisP, yucD, BSU10810 / Plasmid: pET32 Xa/LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21trxB (DE3) References: UniProt: O06728, Transferases; Transferring alkyl or aryl groups, other than methyl groups |
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#2: Chemical | ChemComp-PGE / |
#3: Water | ChemComp-HOH / |
Sequence details | AUTHORS SAY THIS SEQUENCE INCLUDES MATURE PROTEIN OF YISP. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.2 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 9 Details: 1 M LiCl, 0.1 M Bicine pH 9.0, 18-20%(w/v) polyethylene glycol 6000, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 0.97622 Å |
Detector | Type: MX300HE / Detector: CCD / Date: Nov 26, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97622 Å / Relative weight: 1 |
Reflection | Resolution: 1.92→25 Å / Num. obs: 24603 / % possible obs: 99.9 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 32.7 |
Reflection shell | Resolution: 1.92→1.99 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.482 / Mean I/σ(I) obs: 5.5 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 1.92→25 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.92→25 Å
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LS refinement shell | Resolution: 1.92→1.99 Å /
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