+Open data
-Basic information
Entry | Database: PDB / ID: 6kd7 | ||||||
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Title | Crystal structure of geranylgeranyl pyrophosphate synthase | ||||||
Components | Polyprenyl synthetase | ||||||
Keywords | TRANSFERASE / prenyltransferase | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Nonlabens dokdonensis | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å | ||||||
Authors | Kim, S. / Kim, K.-J. | ||||||
Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2019 Title: Crystal structure of geranylgeranyl pyrophosphate synthase (crtE) from Nonlabens dokdonensis DSW-6. Authors: Kim, S. / Kim, E.J. / Park, J.B. / Kim, S.W. / Kim, K.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6kd7.cif.gz | 84.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6kd7.ent.gz | 62.4 KB | Display | PDB format |
PDBx/mmJSON format | 6kd7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kd/6kd7 ftp://data.pdbj.org/pub/pdb/validation_reports/kd/6kd7 | HTTPS FTP |
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-Related structure data
Related structure data | 5jfqS S: Starting model for refinement |
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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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Unit cell |
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-Components
#1: Protein | Mass: 38175.301 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Nonlabens dokdonensis (strain DSM 17205 / KCTC 12402 / DSW-6) (bacteria) Gene: DDD_1788 / Plasmid: pET30a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: L7W5I6 | ||||||
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#2: Chemical | ChemComp-PPV / | ||||||
#3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 7.96 Å3/Da / Density % sol: 84.6 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: Ammonium sulfate, HEPES |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 5, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 78959 / % possible obs: 97.5 % / Redundancy: 10.8 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 28.1 |
Reflection shell | Resolution: 2→2.03 Å / Redundancy: 4 % / Rmerge(I) obs: 0.298 / Mean I/σ(I) obs: 3.3 / Num. unique obs: 3761 / % possible all: 94.8 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5JFQ Resolution: 2→36.43 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.939 / SU B: 3.267 / SU ML: 0.082 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.094 / ESU R Free: 0.096 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 122.49 Å2 / Biso mean: 37.059 Å2 / Biso min: 17.61 Å2
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Refinement step | Cycle: final / Resolution: 2→36.43 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.051 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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