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- PDB-3krc: Mint heterotetrameric geranyl pyrophosphate synthase in complex w... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3krc | ||||||
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Title | Mint heterotetrameric geranyl pyrophosphate synthase in complex with IPP | ||||||
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![]() | TRANSFERASE / prenyltransferase / Isoprene biosynthesis / isoprenyl pyrophosphate synthase | ||||||
Function / homology | ![]() geranyl diphosphate biosynthetic process / prenyltransferase activity / farnesyltranstransferase activity / dimethylallyltranstransferase activity / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Chang, T.-H. / Hsieh, F.-L. / Ko, T.-P. / Wang, A.H.-J. | ||||||
![]() | ![]() 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. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 228.7 KB | Display | ![]() |
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PDB format | ![]() | 182.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 488.9 KB | Display | ![]() |
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Full document | ![]() | 525.6 KB | Display | |
Data in XML | ![]() | 50.7 KB | Display | |
Data in CIF | ![]() | 72.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3kraC ![]() 3krfC ![]() 3kroC ![]() 3krpC ![]() 2j1oS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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). |
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Components
#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.) ![]() ![]() ![]() #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.) ![]() ![]() ![]() #3: Chemical | #4: Chemical | ChemComp-EDO / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.66 % |
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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: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4r / Detector: CCD / Date: Jun 28, 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: 2.3→30 Å / Num. all: 51413 / Num. obs: 46911 / % possible obs: 94.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.2 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 20.8 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 3.1 / Num. unique all: 4403 / % possible all: 89.8 |
-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2J1O Resolution: 2.3→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: 50.304 Å2 | ||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 137.3 Å2 / Biso mean: 54.217 Å2 / Biso min: 17.82 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.38 Å
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Xplor file |
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