+Open data
-Basic information
Entry | Database: PDB / ID: 4c8g | ||||||
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Title | IspF (Burkholderia cenocepacia) CMP 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: 2 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.F. / 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 | 4c8g.cif.gz | 107.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4c8g.ent.gz | 81.5 KB | Display | PDB format |
PDBx/mmJSON format | 4c8g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4c8g_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 4c8g_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 4c8g_validation.xml.gz | 22.6 KB | Display | |
Data in CIF | 4c8g_validation.cif.gz | 31.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c8/4c8g ftp://data.pdbj.org/pub/pdb/validation_reports/c8/4c8g | HTTPS FTP |
-Related structure data
Related structure data | 4c81C 4c82C 4c8eSC 4c8iC 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, 181 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-PO4 / | #5: Chemical | ChemComp-MG / | #6: Water | ChemComp-HOH / | |
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-Details
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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 53 % / Description: NONE |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 Details: HANGING DROP VAPOUR DIFFUSION. BCISPF SAMPLE: 10MG/ML IN 100 MM NACL, 2 MM MGCL2, 100 MM SODIUM FORMATE, PH 5.0, 2 MM CMP. RESERVOIR: 5% W/V PEG 1000, 33% V/V ETHANOL, 0.1 M NA2HPO4, PH 4.0, ...Details: HANGING DROP VAPOUR DIFFUSION. BCISPF SAMPLE: 10MG/ML IN 100 MM NACL, 2 MM MGCL2, 100 MM SODIUM FORMATE, PH 5.0, 2 MM CMP. RESERVOIR: 5% W/V PEG 1000, 33% V/V ETHANOL, 0.1 M NA2HPO4, PH 4.0, 2% V/V DIOXANE. 2 MICROLITERS SAMPLE WERE MIXED WITH 4 MICROLITRES RESERVOIR AT 20 DEGREES C. |
-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: Oct 6, 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→29.84 Å / Num. obs: 38409 / % possible obs: 96 % / Observed criterion σ(I): 2 / Redundancy: 2.6 % / Biso Wilson estimate: 16.5 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 5.9 |
Reflection shell | Resolution: 2→2.1 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 2.7 / % possible all: 95.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4C8E Resolution: 2→29.65 Å / Cor.coef. Fo:Fc: 0.889 / Cor.coef. Fo:Fc free: 0.854 / SU B: 4.058 / SU ML: 0.116 / Cross valid method: THROUGHOUT / ESU R: 0.205 / ESU R Free: 0.186 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES REFINED INDIVIDUALLY. RESIDUES 64-71 CHAIN A ARE DISORDERED. RESIDUES 36, 37 AND ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES REFINED INDIVIDUALLY. RESIDUES 64-71 CHAIN A ARE DISORDERED. RESIDUES 36, 37 AND 65-71 CHAIN B ARE DISORDERED. RESIDUES 66-73 CHAIN C ARE DISORDERED.
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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: 14.53 Å2
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Refinement step | Cycle: LAST / Resolution: 2→29.65 Å
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Refine LS restraints |
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