+Open data
-Basic information
Entry | Database: PDB / ID: 4c8e | ||||||
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Title | IspF (Burkholderia cenocepacia) 2CMP complex | ||||||
Components | 2-C-METHYL-D-ERYTHRITOL 2,4-CYCLODIPHOSPHATE SYNTHASE | ||||||
Keywords | LYASE | ||||||
Function / homology | Function and homology information 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 | BURKHOLDERIA CENOCEPACIA (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | O'Rourke, P.E.F. / Kalinowska-Tluscik, J. / Fyfe, P.K. / Dawson, A. / Hunter, W.N. | ||||||
Citation | Journal: Bmc Struct.Biol. / Year: 2014 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4c8e.cif.gz | 119.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4c8e.ent.gz | 91.9 KB | Display | PDB format |
PDBx/mmJSON format | 4c8e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c8/4c8e ftp://data.pdbj.org/pub/pdb/validation_reports/c8/4c8e | HTTPS FTP |
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-Related structure data
Related structure data | 4c81C 4c82C 4c8gC 4c8iC 3f0gS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 3 molecules ABC
#1: Protein | Mass: 19309.836 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) BURKHOLDERIA CENOCEPACIA (bacteria) / Strain: J2315 / Description: GENOMIC DNA / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): GOLD References: UniProt: B4EC22, 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase |
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-Non-polymers , 5 types, 431 molecules
#2: Chemical | #3: Chemical | ChemComp-C5P / #4: Chemical | ChemComp-SO4 / | #5: Chemical | ChemComp-PEG / | #6: Water | ChemComp-HOH / | |
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-Details
Nonpolymer details | CYTIDINE-5'-MONOPHOSPHSequence 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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54 % / Description: NONE |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 Details: PROTEIN WAS CRYSTALLISED BY HANGING-DROP VAPOUR DIFFUSION. BCISPF SAMPLE IN 100 MM NACL, 2MM MGCL2, 100 MM TRIS-HCL, PH 7.5; WAS CONCENTRATED TO 5 MG/ML, AND HAD CMP ADDED (20 MM ...Details: PROTEIN WAS CRYSTALLISED BY HANGING-DROP VAPOUR DIFFUSION. BCISPF SAMPLE IN 100 MM NACL, 2MM MGCL2, 100 MM TRIS-HCL, PH 7.5; WAS CONCENTRATED TO 5 MG/ML, AND HAD CMP ADDED (20 MM CONCENTRATION IN SAMPLE). CRYSTALS WERE OBTAINED BY MIXING 2 MICROLITRES OF SAMPLE WITH 2 MICROLITRES RESERVOIR AT 20 DEGREES C. RESERVOIR SOLUTION: 25% W/V PEG 3350, 2.2M (NH4)2SO4, 0.1 M SODIUM FORMATE, PH 5.0, 1% V/V DIOXANE. CRYO: 20% GLYCEROL. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IV PLUS PLUS / Detector: IMAGE PLATE / Date: Apr 5, 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: 1.9→19.32 Å / Num. obs: 47918 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Biso Wilson estimate: 16.3 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 6.2 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 3.1 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3F0G Resolution: 1.9→70.76 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.902 / SU B: 3.529 / SU ML: 0.105 / Cross valid method: THROUGHOUT / ESU R: 0.152 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 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: 17.204 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→70.76 Å
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Refine LS restraints |
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