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Yorodumi- PDB-4lfe: Crystal structure of geranylgeranyl diphosphate synthase sub1274 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4lfe | ||||||
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Title | Crystal structure of geranylgeranyl diphosphate synthase sub1274 (target efi-509455) from streptococcus uberis 0140j with bound magnesium and isopentyl diphosphate, partially liganded complex; | ||||||
Components | Geranylgeranyl diphosphate synthase | ||||||
Keywords | TRANSFERASE / ISOPRENOID SYNTHASE / ENZYME FUNCTION INITIATIVE / EFI / Structural Genomics | ||||||
Function / homology | Function and homology information (2E,6E)-farnesyl diphosphate synthase / geranyltranstransferase activity / isoprenoid biosynthetic process Similarity search - Function | ||||||
Biological species | Streptococcus uberis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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. / 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 Geranylgeranyl Diphosphate Synthase from Streptococcus Uberis 0140J Authors: Patskovsky, Y. / Toro, R. / Bhosle, R. / Hillerich, B. / Seidel, R.D. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / Imker, H.J. / Al Obaidi, N. / Stead, M. ...Authors: Patskovsky, Y. / Toro, R. / Bhosle, R. / Hillerich, B. / Seidel, R.D. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / 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 | 4lfe.cif.gz | 235.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4lfe.ent.gz | 190.3 KB | Display | PDB format |
PDBx/mmJSON format | 4lfe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lf/4lfe ftp://data.pdbj.org/pub/pdb/validation_reports/lf/4lfe | HTTPS FTP |
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-Related structure data
Related structure data | 4lfgC 4gp1S C: citing same article (ref.) 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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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 32298.201 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus uberis (bacteria) / Strain: 0140J / Gene: fps, SUB1274 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RIL References: UniProt: B9DUT7, (2E,6E)-farnesyl diphosphate synthase #2: Chemical | #3: Chemical | ChemComp-MG / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.59 Å3/Da / Density % sol: 52.56 % |
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Crystal grow | pH: 6.5 Details: 0.2M MAGNESIUM CHLORIDE, 0.1M MES-NAOH, PH 6.5, 25% PEG4000, 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 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 18, 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: 1.95→50 Å / Num. obs: 48833 / % possible obs: 98.8 % / Observed criterion σ(I): -5 / Redundancy: 8.2 % / Biso Wilson estimate: 24.882 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 1.95→1.98 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 4.1 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4GP1 Resolution: 1.95→46.82 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.944 / SU B: 8.413 / SU ML: 0.121 / Cross valid method: THROUGHOUT / ESU R: 0.168 / ESU R Free: 0.148 / 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: 37.708 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→46.82 Å
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Refine LS restraints |
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