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Yorodumi- PDB-4jxn: CRYSTAL STRUCTURE OF POLYPRENYL SYNTHASE ISP_B (TARGET EFI-509198... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4jxn | ||||||
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Title | CRYSTAL STRUCTURE OF POLYPRENYL SYNTHASE ISP_B (TARGET EFI-509198) FROM Roseobacter denitrificans | ||||||
Components | Octaprenyl-diphosphate synthase | ||||||
Keywords | TRANSFERASE / ISOPRENOID SYNTHASE / ENZYME FUNCTION INITIATIVE / EFI / Structural Genomics | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Roseobacter denitrificans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Patskovsky, Y. / Toro, R. / Bhosle, R. / Hillerich, B. / Seidel, R.D. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. ...Patskovsky, Y. / Toro, R. / Bhosle, R. / Hillerich, B. / Seidel, R.D. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / Zencheck, W.D. / Imker, H.J. / Al Obaidi, N. / Stead, M. / Love, J. / Poulter, C.D. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI) | ||||||
Citation | Journal: To be Published Title: Crystal Structure of Isoprenoid Synthase Isp_B from Roseobacter Denitrificans Authors: Patskovsky, Y. / Toro, R. / Bhosle, R. / Hillerich, B. / Seidel, R.D. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / Zencheck, W.D. / Imker, H.J. / Al ...Authors: Patskovsky, Y. / Toro, R. / Bhosle, R. / Hillerich, B. / Seidel, R.D. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / Zencheck, W.D. / Imker, H.J. / Al Obaidi, N. / Stead, M. / Love, J. / Poulter, C.D. / Gerlt, J.A. / Almo, S.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4jxn.cif.gz | 71.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4jxn.ent.gz | 52.4 KB | Display | PDB format |
PDBx/mmJSON format | 4jxn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jx/4jxn ftp://data.pdbj.org/pub/pdb/validation_reports/jx/4jxn | HTTPS FTP |
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-Related structure data
Related structure data | 4gp1S S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 36124.070 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Roseobacter denitrificans (bacteria) / Strain: ATCC 33942 / OCh 114 / Gene: ispB, RD1_3401 / Plasmid: PET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q163F0 |
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#2: Chemical | ChemComp-UNL / Num. of mol.: 1 / Source method: obtained synthetically |
#3: Chemical | ChemComp-CL / |
#4: Water | ChemComp-HOH / |
Nonpolymer details | THE NATURE OF THE UNL LIGAND IS UNKNOWN; HOWEVER, IT IS LIKELY TO BE AN ISOPRENOID-RELATED SMALL ...THE NATURE OF THE UNL LIGAND IS UNKNOWN; HOWEVER, IT IS LIKELY TO BE AN ISOPRENOID |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.64 Å3/Da / Density % sol: 53.36 % |
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Crystal grow | pH: 4.6 Details: 0.2M CALCIUM CHLORIDE, 0.1M SODIUM ACETATE, PH 4.6, 30% PEG400, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 21, 2013 / Details: MIRRORS |
Radiation | Monochromator: ROSENBAUM-ROCK DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.075 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 17070 / % possible obs: 98 % / Observed criterion σ(I): -5 / Redundancy: 9 % / Rmerge(I) obs: 0.111 / Net I/σ(I): 7.3 |
Reflection shell | Resolution: 2.3→2.34 Å / Redundancy: 8.7 % / Mean I/σ(I) obs: 1.5 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4GP1 Resolution: 2.3→35.68 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.932 / SU B: 10.383 / SU ML: 0.236 / Cross valid method: THROUGHOUT / ESU R: 0.287 / ESU R Free: 0.247 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 81.29 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→35.68 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.36 Å / Total num. of bins used: 20
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