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Open data
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Basic information
Entry | Database: PDB / ID: 6r05 | |||||||||
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Title | T. CRUZI FPPS IN COMPLEX WITH N-BENZYL-6-METHYLPYRIDIN-2-AMINE | |||||||||
![]() | Farnesyl diphosphate synthase | |||||||||
![]() | TRANSFERASE / farnesyl diphosphate synthase / sterol biosynthesis / farnesyl pyrophosphate / homodimer | |||||||||
Function / homology | ![]() farnesyl diphosphate biosynthetic process / dimethylallyltranstransferase activity / geranyltranstransferase activity / membrane / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() ![]() | |||||||||
![]() | Petrick, J.K. / Muenzker, L. / Schleberger, C. / Jahnke, W. | |||||||||
Funding support | 2items
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![]() | ![]() Title: Targeting farnesyl pyrophosphate synthase of Trypanosoma cruzi by fragment-based lead discovery Authors: Petrick, J.K. / Jahnke, W. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 161.8 KB | Display | ![]() |
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PDB format | ![]() | 125.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 712.2 KB | Display | ![]() |
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Full document | ![]() | 712.3 KB | Display | |
Data in XML | ![]() | 16.8 KB | Display | |
Data in CIF | ![]() | 25.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6r04C ![]() 6r06C ![]() 6r07C ![]() 6r08C ![]() 6r09C ![]() 6r0aC ![]() 6r0bC ![]() 6r39C ![]() 6shvC ![]() 6si5C ![]() 4dwgS 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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1 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 41359.574 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Termini not resolved / Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 6 types, 269 molecules ![](data/chem/img/JNE.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-JNE / | ||||
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#3: Chemical | ChemComp-SO4 / | ||||
#4: Chemical | ChemComp-DMS / | ||||
#5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.54 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 80 mM MES, 8.5 mM ZnSO4, 19.42% PEG MME 550, 15% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 15, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99981 Å / Relative weight: 1 |
Reflection | Resolution: 1.568→66.115 Å / Num. obs: 57627 / % possible obs: 100 % / Redundancy: 18 % / Biso Wilson estimate: 28.45 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.024 / Rrim(I) all: 0.102 / Rsym value: 0.099 / Net I/σ(I): 15.1 |
Reflection shell | Resolution: 1.568→1.595 Å / Redundancy: 18.3 % / Rmerge(I) obs: 3.102 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 2762 / CC1/2: 0.417 / Rpim(I) all: 0.741 / Rrim(I) all: 3.19 / Rsym value: 3.102 / % possible all: 100 |
-Phasing
Phasing | Method: ![]() | ||||||
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Phasing MR | Model details: Phaser MODE: MR_TRA
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4DWG Resolution: 1.57→22.62 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.955 / SU R Cruickshank DPI: 0.076 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.081 / SU Rfree Blow DPI: 0.08 / SU Rfree Cruickshank DPI: 0.076
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Displacement parameters | Biso max: 117.82 Å2 / Biso mean: 35.17 Å2 / Biso min: 17.96 Å2
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Refine analyze | Luzzati coordinate error obs: 0.22 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.57→22.62 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.57→1.58 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
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Refinement TLS params. | Method: refined / Origin x: -8.2944 Å / Origin y: -17.7865 Å / Origin z: -20.3451 Å
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Refinement TLS group | Selection details: { A|* } |