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- PDB-6r06: T. CRUZI FPPS IN COMPLEX WITH (3S,4S)-4-(3,4-dimethylphenoxy)-1-(... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6r06 | ||||||
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Title | T. CRUZI FPPS IN COMPLEX WITH (3S,4S)-4-(3,4-dimethylphenoxy)-1-(prop-2-yn-1-yl)piperidin-3-ol | ||||||
![]() | 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. / Wolfgang, J. | ||||||
Funding support | 1items
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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 | ![]() | 166.6 KB | Display | ![]() |
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PDB format | ![]() | 129.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6r04C ![]() 6r05C ![]() 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 , 5 types, 256 molecules ![](data/chem/img/JMN.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-ACT / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.4 % |
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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: Jun 10, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99999 Å / Relative weight: 1 |
Reflection | Resolution: 1.559→50.286 Å / Num. obs: 58053 / % possible obs: 99 % / Redundancy: 17.8 % / Biso Wilson estimate: 28.19 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.024 / Rrim(I) all: 0.1 / Rsym value: 0.097 / Net I/σ(I): 15.5 |
Reflection shell | Resolution: 1.559→1.586 Å / Redundancy: 18.1 % / Rmerge(I) obs: 3.043 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 2851 / CC1/2: 0.342 / Rpim(I) all: 0.731 / Rrim(I) all: 3.13 / Rsym value: 3.043 / % 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: 1.559→50.286 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.945 / SU R Cruickshank DPI: 0.082 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.087 / SU Rfree Blow DPI: 0.086 / SU Rfree Cruickshank DPI: 0.082
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Displacement parameters | Biso max: 111.65 Å2 / Biso mean: 36.93 Å2 / Biso min: 15.75 Å2
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Refine analyze | Luzzati coordinate error obs: 0.23 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.559→50.286 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.56→1.57 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
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Refinement TLS params. | Method: refined / Origin x: -9.908 Å / Origin y: -17.0261 Å / Origin z: -20.4152 Å
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Refinement TLS group | Selection details: { A|* } |