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- PDB-3krp: Mint heterotetrameric geranyl pyrophosphate synthase in complex w... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3krp | ||||||
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Title | Mint heterotetrameric geranyl pyrophosphate synthase in complex with magnesium and GPP | ||||||
![]() | (Geranyl diphosphate synthase ...) x 2 | ||||||
![]() | 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. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 234 KB | Display | ![]() |
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PDB format | ![]() | 184.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3kraC ![]() 3krcC ![]() 3krfC ![]() 3kroC ![]() 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
-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.) ![]() ![]() ![]() #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.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 823 molecules ![](data/chem/img/PPV.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/GPP.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/GPP.gif)
![](data/chem/img/HOH.gif)
#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: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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