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- PDB-3oab: Mint deletion mutant of heterotetrameric geranyl pyrophosphate sy... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3oab | |||||||||
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Title | Mint deletion mutant of heterotetrameric geranyl pyrophosphate synthase in complex with ligands | |||||||||
![]() | (Geranyl diphosphate synthase ...) x 2 | |||||||||
![]() | TRANSFERASE / prenyltransferase / All alpha-helices fold / monoterpene biosynthesis / chroloplast | |||||||||
Function / homology | ![]() geranyl diphosphate biosynthetic process / prenyltransferase activity / farnesyltranstransferase activity / dimethylallyltranstransferase activity / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() ![]() | |||||||||
![]() | Hsieh, F.-L. / Chang, T.-H. / Ko, T.-P. / Wang, A.H.-J. | |||||||||
![]() | ![]() Title: Enhanced specificity of mint geranyl pyrophosphate synthase by modifying the R-loop interactions Authors: Hsieh, F.-L. / Chang, T.-H. / Ko, T.-P. / 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 | ![]() | 227.8 KB | Display | ![]() |
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PDB format | ![]() | 180 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3oacC ![]() 3krfS S: Starting model for refinement C: citing same article ( |
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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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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: 28712.795 Da / Num. of mol.: 2 / Fragment: UNP residues 49-313 / Mutation: DELETION Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 6 types, 645 molecules ![](data/chem/img/PPV.gif)
![](data/chem/img/DST.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/IPE.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/DST.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/IPE.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-PPV / | ||||||||
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#4: Chemical | #5: Chemical | ChemComp-MG / #6: Chemical | ChemComp-EDO / | #7: Chemical | ChemComp-IPE / | #8: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.69 % |
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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 315 / Detector: CCD / Date: Jan 1, 2009 |
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. obs: 50303 / % possible obs: 98.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.2 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 19.8 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.436 / Mean I/σ(I) obs: 3.2 / Num. unique all: 4383 / % possible all: 95.1 |
-Phasing
Phasing | Method: ![]() |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3KRF Resolution: 2.3→24.96 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: 31.0722 Å2 | ||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 128.32 Å2 / Biso mean: 41.2865 Å2 / Biso min: 7.89 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→24.96 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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