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Open data
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Basic information
Entry | Database: PDB / ID: 4c8i | ||||||
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Title | IspF (Burkholderia cenocepacia) citrate complex | ||||||
![]() | 2-C-METHYL-D-ERYTHRITOL 2,4-CYCLODIPHOSPHATE SYNTHASE | ||||||
![]() | LYASE | ||||||
Function / homology | ![]() 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.F. / Kalinowska-Tluscik, J. / Fyfe, P.K. / Dawson, A. / Hunter, W.N. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 111.2 KB | Display | ![]() |
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PDB format | ![]() | 84.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 486.8 KB | Display | ![]() |
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Full document | ![]() | 495.9 KB | Display | |
Data in XML | ![]() | 24 KB | Display | |
Data in CIF | ![]() | 33.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4c81C ![]() 4c82C ![]() 4c8eSC ![]() 4c8gC C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 19309.836 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: B4EC22, 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-PO4 / | #5: Water | ChemComp-HOH / | Nonpolymer details | CITRIC ACID (CIT): ONLY CITRATE D1 IS AT FULL OCCUPANCY | Sequence details | ALTHOUGH RESIDUE 3 IS LISTED AS PHENYLALANINE IN THE UNIPROT DATABASE, IT WAS FOUND TO BE VALINE ...ALTHOUGH RESIDUE 3 IS LISTED AS PHENYLALAN | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 43 % / Description: NONE |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 Details: SITTING DROP VAPOUR DIFFUSION. BCISPF SAMPLE: 10MG/ML IN 100 MM NACL, 100 MM SODIUM FORMATE, PH 5.0. RESERVOIR: 5% W/V PEG 1000, 36% V/V ETHANOL, 100 MM NA2HPO4, 100MM CITRIC ACID, PH 4.2. 1. ...Details: SITTING DROP VAPOUR DIFFUSION. BCISPF SAMPLE: 10MG/ML IN 100 MM NACL, 100 MM SODIUM FORMATE, PH 5.0. RESERVOIR: 5% W/V PEG 1000, 36% V/V ETHANOL, 100 MM NA2HPO4, 100MM CITRIC ACID, PH 4.2. 1.5 MICROLITRES OF SAMPLE WERE MIXED WITH 3 MICROLITRES RESERVOIR AT 20 DEGREES C. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV PLUS PLUS / Detector: IMAGE PLATE / Date: Jun 14, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→40.9 Å / Num. obs: 33460 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Biso Wilson estimate: 18.7 Å2 / Rmerge(I) obs: 0.03 / Net I/σ(I): 23.9 |
Reflection shell | Resolution: 2→2.1 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.08 / Mean I/σ(I) obs: 12.8 / % possible all: 96.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4C8E Resolution: 2→22.81 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.933 / SU B: 2.805 / SU ML: 0.081 / Cross valid method: THROUGHOUT / ESU R: 0.157 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 64-73 CHAIN A ARE DISORDERED. RESIDUES 63-69 CHAIN C ARE DISORDERED. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.918 Å2
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Refinement step | Cycle: LAST / Resolution: 2→22.81 Å
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Refine LS restraints |
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