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Yorodumi- PDB-4llt: Crystal structure of a farnesyl diphosphate synthase from Roseoba... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4llt | ||||||
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Title | Crystal structure of a farnesyl diphosphate synthase from Roseobacter denitrificans OCh 114, target EFI-509393, with two IPP and calcium bound in active site | ||||||
Components | Geranyltranstransferase | ||||||
Keywords | TRANSFERASE / Structural Genomics / Enzyme Function Initiative / polyprenyl synthetase | ||||||
Function / homology | Function and homology information (2E,6E)-farnesyl diphosphate synthase / geranyltranstransferase activity / isoprenoid biosynthetic process / metal ion binding Similarity search - Function | ||||||
Biological species | Roseobacter denitrificans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å | ||||||
Authors | Kim, J. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Washington, E. / Scott Glenn, A. / Chowdhury, S. ...Kim, J. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / Hillerich, B. / Love, J. / Seidel, R.D. / Imker, H.J. / Stead, M. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI) | ||||||
Citation | Journal: To be Published Title: Crystal structure of a farnesyl diphosphate synthase from Roseobacter denitrificans OCh 114, target EFI-509393, with two IPP and calcium bound in active site Authors: Kim, J. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / Hillerich, B. ...Authors: Kim, J. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / Hillerich, B. / Love, J. / Seidel, R.D. / Imker, H.J. / Stead, M. / 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 | 4llt.cif.gz | 131.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4llt.ent.gz | 100 KB | Display | PDB format |
PDBx/mmJSON format | 4llt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ll/4llt ftp://data.pdbj.org/pub/pdb/validation_reports/ll/4llt | HTTPS FTP |
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-Related structure data
Related structure data | 3lvsS 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 domain:
NCS domain segments: Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: THR / End label comp-ID: THR / Refine code: 0 / Auth seq-ID: 0 - 288 / Label seq-ID: 22 - 310
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-Components
#1: Protein | Mass: 32847.074 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Roseobacter denitrificans (bacteria) / Strain: ATCC 33942 / OCh 114 / Gene: ispA, RD1_0549 / Plasmid: pSGC-His / Production host: Escherichia coli (E. coli) References: UniProt: Q16CN9, (2E,6E)-farnesyl diphosphate synthase #2: Chemical | ChemComp-IPE / #3: Chemical | ChemComp-CA / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.38 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 0.2 M calcium acetate, 0.1 M MES/NaOH, pH 6, 20% v/v PEG8000, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Jun 14, 2013 |
Radiation | Monochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→50 Å / Num. all: 81341 / Num. obs: 78181 / % possible obs: 96.1 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 16.2 |
Reflection shell | Resolution: 1.55→1.58 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.684 / Mean I/σ(I) obs: 2.1 / % possible all: 93.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3LVS Resolution: 1.55→26.46 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.949 / SU B: 1.407 / SU ML: 0.051 / Cross valid method: THROUGHOUT / ESU R: 0.081 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.307 Å2
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Refinement step | Cycle: LAST / Resolution: 1.55→26.46 Å
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Refine LS restraints |
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