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Yorodumi- PDB-3ikf: Crystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ikf | ||||||
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Title | Crystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from Burkholderia pseudomallei with FOL fragment 717, imidazo[2,,1-b][1,3]thiazol-6-ylmethanol | ||||||
Components | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase | ||||||
Keywords | LYASE / NIAID / SSGCID / Seattle Structural Genomics Center for Infectious Disease / fragment-based drug design / FBDD / Isoprene biosynthesis / Metal-binding | ||||||
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 pseudomallei (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.07 Å | ||||||
Authors | Seattle Structural Genomics Center for Infectious Disease (SSGCID) | ||||||
Citation | Journal: J Struct Funct Genomics / Year: 2011 Title: Leveraging structure determination with fragment screening for infectious disease drug targets: MECP synthase from Burkholderia pseudomallei. Authors: Begley, D.W. / Hartley, R.C. / Davies, D.R. / Edwards, T.E. / Leonard, J.T. / Abendroth, J. / Burris, C.A. / Bhandari, J. / Myler, P.J. / Staker, B.L. / Stewart, L.J. #1: Journal: Plos One / Year: 2013 Title: Combining functional and structural genomics to sample the essential Burkholderia structome. Authors: Baugh, L. / Gallagher, L.A. / Patrapuvich, R. / Clifton, M.C. / Gardberg, A.S. / Edwards, T.E. / Armour, B. / Begley, D.W. / Dieterich, S.H. / Dranow, D.M. / Abendroth, J. / Fairman, J.W. / ...Authors: Baugh, L. / Gallagher, L.A. / Patrapuvich, R. / Clifton, M.C. / Gardberg, A.S. / Edwards, T.E. / Armour, B. / Begley, D.W. / Dieterich, S.H. / Dranow, D.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Staker, B.L. / Phan, I. / Gillespie, A. / Choi, R. / Nakazawa-Hewitt, S. / Nguyen, M.T. / Napuli, A. / Barrett, L. / Buchko, G.W. / Stacy, R. / Myler, P.J. / Stewart, L.J. / Manoil, C. / Van Voorhis, W.C. #2: Journal: Bioorg.Med.Chem.Lett. / Year: 2013 Title: Cytidine derivatives as IspF inhibitors of Burkolderia pseudomallei. Authors: Zhang, Z. / Jakkaraju, S. / Blain, J. / Gogol, K. / Zhao, L. / Hartley, R.C. / Karlsson, C.A. / Staker, B.L. / Edwards, T.E. / Stewart, L.J. / Myler, P.J. / Clare, M. / Begley, D.W. / Horn, J.R. / Hagen, T.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ikf.cif.gz | 108 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ikf.ent.gz | 81.9 KB | Display | PDB format |
PDBx/mmJSON format | 3ikf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ikf_validation.pdf.gz | 473.1 KB | Display | wwPDB validaton report |
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Full document | 3ikf_full_validation.pdf.gz | 476.5 KB | Display | |
Data in XML | 3ikf_validation.xml.gz | 21.9 KB | Display | |
Data in CIF | 3ikf_validation.cif.gz | 31.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ik/3ikf ftp://data.pdbj.org/pub/pdb/validation_reports/ik/3ikf | HTTPS FTP |
-Related structure data
Related structure data | 3f0dC 3f0eSC 3f0gC 3ieqC 3iewC 3ikeC 3jvhC 3k14C 3k2xC 3mbmC 3p0zC 3p10C 3qhdC C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-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, 3 molecules ABC
#1: Protein | Mass: 17495.881 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia pseudomallei (bacteria) / Strain: 1710b / Gene: ispF, mecS, BPSL2098 / Production host: Escherichia coli (E. coli) References: UniProt: Q63T71, 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase |
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-Non-polymers , 6 types, 319 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-CL / | #5: Chemical | ChemComp-ACT / | #6: Chemical | ChemComp-K / | #7: Water | ChemComp-HOH / | |
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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: 2.25 Å3/Da / Density % sol: 45.38 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.9 Details: 20% PEG 3350, 0.2 M Mg formate, 34.4 mg/mL protein, 20 mM FOL 717, 10 mM ZnCl2, pH 5.9, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Jul 31, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.07→20 Å / Num. obs: 26980 / % possible obs: 94.4 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 28.092 Å2 / Rmerge(I) obs: 0.033 / Net I/σ(I): 30.29 |
Reflection shell | Resolution: 2.07→2.12 Å / Rmerge(I) obs: 0.141 / Mean I/σ(I) obs: 8.7 / Num. measured obs: 5612 / Num. unique all: 1735 / Num. unique obs: 1735 / % possible all: 82.8 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3F0E Resolution: 2.07→19.49 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.927 / WRfactor Rfree: 0.206 / WRfactor Rwork: 0.161 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.846 / SU B: 4.55 / SU ML: 0.123 / SU R Cruickshank DPI: 0.226 / SU Rfree: 0.182 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.226 / ESU R Free: 0.182 / 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: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 68.27 Å2 / Biso mean: 23.615 Å2 / Biso min: 4.09 Å2
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Refinement step | Cycle: LAST / Resolution: 2.07→19.49 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.07→2.123 Å / Total num. of bins used: 20
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