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Yorodumi- PDB-3krp: Mint heterotetrameric geranyl pyrophosphate synthase in complex w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3krp | ||||||
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Title | Mint heterotetrameric geranyl pyrophosphate synthase in complex with magnesium and GPP | ||||||
Components | (Geranyl diphosphate synthase ...) x 2 | ||||||
Keywords | TRANSFERASE / prenyltransferase / Isoprene biosynthesis / isoprenyl pyrophosphate synthase | ||||||
Function / homology | Function and homology information geranyl diphosphate biosynthetic process / dimethylallyltranstransferase activity / metal ion binding Similarity search - Function | ||||||
Biological species | Mentha x piperita (peppermint) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.42 Å | ||||||
Authors | Chang, T.-H. / Hsieh, F.-L. / Ko, T.-P. / Wang, A.H.-J. | ||||||
Citation | Journal: Plant Cell / Year: 2010 Title: Structure of a heterotetrameric geranyl pyrophosphate synthase from mint (Mentha piperita) reveals intersubunit regulation Authors: Chang, T.-H. / Hsieh, F.-L. / Ko, T.-P. / Teng, K.-H. / Liang, P.-H. / Wang, A.H.-J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3krp.cif.gz | 234 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3krp.ent.gz | 184.6 KB | Display | PDB format |
PDBx/mmJSON format | 3krp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kr/3krp ftp://data.pdbj.org/pub/pdb/validation_reports/kr/3krp | HTTPS FTP |
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-Related structure data
Related structure data | 3kraC 3krcC 3krfC 3kroC 2j1oS C: citing same article (ref.) 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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3 |
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Unit cell |
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Details | Gel filtration chromatography demonstrate that the biological assembly should be a hetero-tetramer, composed of two hetero-dimers (one is A chain and B chain, the other is C chain and D chain). |
-Components
-Geranyl diphosphate synthase ... , 2 types, 4 molecules ADBC
#1: Protein | Mass: 31947.004 Da / Num. of mol.: 2 / Fragment: UNP residues 84-377 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mentha x piperita (peppermint) / Gene: GPPS Large Subunit / Plasmid: pET32 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9SBR3, dimethylallyltranstransferase #2: Protein | Mass: 29755.963 Da / Num. of mol.: 2 / Fragment: UNP residues 49-313 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mentha x piperita (peppermint) / Gene: GPPS Small subunit / Plasmid: pET37 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9SBR4, dimethylallyltranstransferase |
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-Non-polymers , 5 types, 823 molecules
#3: Chemical | ChemComp-PPV / | ||||||
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#4: Chemical | ChemComp-MG / #5: Chemical | ChemComp-EDO / | #6: Chemical | ChemComp-GPP / | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.6 % / Mosaicity: 0.622 ° |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion / pH: 6.5 Details: 100mM Bis-Tris, 200mM ammonium acetate, 20% PEG 3350, pH 6.5, vapor diffusion, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 29, 2008 |
Radiation | Monochromator: Horizontally Focusing Single Crystal Monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→30 Å / Num. all: 56022 / Num. obs: 51803 / % possible obs: 99.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.9 % / Rmerge(I) obs: 0.077 / Χ2: 1.006 / Net I/σ(I): 16.7 |
Reflection shell | Resolution: 2.25→2.33 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.543 / Mean I/σ(I) obs: 2.1 / Num. unique all: 5105 / Χ2: 0.934 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2J1O Resolution: 2.42→30 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 57.065 Å2 | ||||||||||||||||||||||||||||
Displacement parameters | Biso max: 146.17 Å2 / Biso mean: 54.754 Å2 / Biso min: 18.55 Å2
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Refinement step | Cycle: LAST / Resolution: 2.42→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.42→2.53 Å /
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Xplor file |
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