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Open data
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Basic information
Entry | Database: PDB / ID: 4c81 | ||||||
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Title | IspF (Plasmodium falciparum) CDP complex | ||||||
![]() | 2-C-METHYL-D-ERYTHRITOL 2,4-CYCLODIPHOSPHATE SYNTHASE | ||||||
![]() | LYASE | ||||||
Function / homology | ![]() apicoplast / 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase / 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase activity / isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway / terpenoid biosynthetic process / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | O'Rourke, P.E.F. / Kalinowska-Tluscik, J. / Fyfe, P.K. / Dawson, A. / Hunter, W.N. | ||||||
![]() | ![]() Title: Crystal Structures of Ispf from Plasmodium Falciparum and Burkholderia Cenocepacia: Comparisons Inform Antimicrobial Drug Target Assessment. Authors: O Rourke, P.E. / Kalinowska-Tluscik, J. / Fyfe, P.K. / Dawson, A. / Hunter, W.N. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 52.1 KB | Display | ![]() |
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PDB format | ![]() | 35.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 9.6 KB | Display | |
Data in CIF | ![]() | 12.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4c82C ![]() 4c8eC ![]() 4c8gC ![]() 4c8iC ![]() 1gx1S 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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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 20574.588 Da / Num. of mol.: 1 Fragment: MATURE PROTEIN (APICOPLAST-TARGETING SEQUENCE OMITTED), RESIDUES 60-240 Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: 3D7 / Description: SYNTHETIC GENE / Plasmid: PET15BTEV / Production host: ![]() ![]() References: UniProt: P62368, 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase |
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-Non-polymers , 5 types, 92 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/CDP.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CDP.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-CDP / | #4: Chemical | #5: Chemical | ChemComp-SO4 / | #6: Water | ChemComp-HOH / | |
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-Details
Sequence details | RESIDUES 1-59, A PREDICTED APICOPLAST TARGETING SEQUENCE, HAVE BEEN OMITTED FROM THE CONSTRUCT USED ...RESIDUES 1-59, A PREDICTED APICOPLAST |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.4 Å3/Da / Density % sol: 63 % / Description: NONE |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: PROTEIN WAS CRYSTALLISED BY HANGING-DROP VAPOUR DIFFUSION. PFISPF SAMPLE IN 100 MM KCL, 100 MM L-ARGININE, 2 MM MGCL2, 50 MM CHES, PH 9.5; WAS CONCENTRATED TO 6 MG/ML, AND HAD CDP DISODIUM ...Details: PROTEIN WAS CRYSTALLISED BY HANGING-DROP VAPOUR DIFFUSION. PFISPF SAMPLE IN 100 MM KCL, 100 MM L-ARGININE, 2 MM MGCL2, 50 MM CHES, PH 9.5; WAS CONCENTRATED TO 6 MG/ML, AND HAD CDP DISODIUM SALT ADDED (2 MM FINAL CONCENTRATION). CRYSTALS WERE OBTAINED BY MIXING 2 MICROLITES OF PROTEIN WITH 2 MICROLITRES OF RESERVOIR SOLUTION AT 20 DEGREES C. RESERVOIR SOLUTION: 1.8-2.5 M (NH4)2SO4, 5MM ZNCL2, 100 MM BIS-TRIS, PH 5.5. SATURATED SUCROSE WAS USED AS A CRYO-PROTECTANT DURING COLLECTION. |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 14, 2009 | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 0.9841 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 1.6→41.63 Å / Num. obs: 35607 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 5.1 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 11.1 | |||||||||||||||
Reflection shell | Resolution: 1.6→1.69 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 2.6 / % possible all: 99.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1GX1 Resolution: 1.56→26.38 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.077 / SU ML: 0.034 / Cross valid method: THROUGHOUT / ESU R: 0.011 / ESU R Free: 0.012 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. RESIDUES 83-97 AND 144-151 ARE DISORDERED.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.949 Å2
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Refinement step | Cycle: LAST / Resolution: 1.56→26.38 Å
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Refine LS restraints |
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