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Yorodumi- PDB-7cpm: CRYSTAL STRUCTURE OF DODECAPRENYL DIPHOSPHATE SYNTHASE FROM THERM... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7cpm | ||||||
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Title | CRYSTAL STRUCTURE OF DODECAPRENYL DIPHOSPHATE SYNTHASE FROM THERMOBIFIDA FUSCA | ||||||
Components | Trans,polycis-polyprenyl diphosphate synthase ((2Z,6E)-farnesyl diphosphate specific) | ||||||
Keywords | TRANSFERASE / prenyltransferase | ||||||
Function / homology | trans,polycis-polyprenyl diphosphate synthase [(2Z,6E)-farnesyl diphosphate specific] / Di-trans-poly-cis-decaprenylcistransferase-like, conserved site / Undecaprenyl pyrophosphate synthase family signature. / Decaprenyl diphosphate synthase-like / Putative undecaprenyl diphosphate synthase / Decaprenyl diphosphate synthase-like superfamily / prenyltransferase activity / magnesium ion binding / Trans,polycis-polyprenyl diphosphate synthase ((2Z,6E)-farnesyl diphosphate specific) Function and homology information | ||||||
Biological species | Thermobifida fusca (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Kurokawa, H. / Ambo, T. / Takahashi, S. / Koyama, T. | ||||||
Funding support | Japan, 1items
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Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2020 Title: Crystal structure of Thermobifida fusca cis-prenyltransferase reveals the dynamic nature of its RXG motif-mediated inter-subunit interactions critical for its catalytic activity. Authors: Kurokawa, H. / Ambo, T. / Takahashi, S. / Koyama, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7cpm.cif.gz | 525.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7cpm.ent.gz | 440.2 KB | Display | PDB format |
PDBx/mmJSON format | 7cpm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7cpm_validation.pdf.gz | 472.3 KB | Display | wwPDB validaton report |
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Full document | 7cpm_full_validation.pdf.gz | 483.8 KB | Display | |
Data in XML | 7cpm_validation.xml.gz | 50.3 KB | Display | |
Data in CIF | 7cpm_validation.cif.gz | 69.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cp/7cpm ftp://data.pdbj.org/pub/pdb/validation_reports/cp/7cpm | HTTPS FTP |
-Related structure data
Related structure data | 7cpnC 1f75S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 32645.795 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermobifida fusca (strain YX) (bacteria) Strain: YX / Gene: Tfu_0853 / Production host: Escherichia coli (E. coli) References: UniProt: Q47RM6, trans,polycis-polyprenyl diphosphate synthase [(2Z,6E)-farnesyl diphosphate specific] #2: 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: 2.1 Å3/Da / Density % sol: 41.46 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 0.1 M citric acid sodium citrate, 5% PEG6000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 7, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→49.409 Å / Num. obs: 52305 / % possible obs: 99.8 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 46.201 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.371 / Mean I/σ(I) obs: 5.124 / Num. unique obs: 5149 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1F75 Resolution: 2.6→49.409 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.933 / WRfactor Rfree: 0.236 / WRfactor Rwork: 0.19 / Average fsc free: 0.9125 / Average fsc work: 0.9294 / Cross valid method: FREE R-VALUE / ESU R: 1.173 / ESU R Free: 0.302 Details: Hydrogens have been added in their 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: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 63.085 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→49.409 Å
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Refine LS restraints |
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LS refinement shell |
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