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Yorodumi- PDB-1knk: Crystal Structure of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1knk | ||||||
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Title | Crystal Structure of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate Synthase (ispF) from E. coli involved in Mevalonate-Independent Isoprenoid Biosynthesis | ||||||
Components | 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase | ||||||
Keywords | METAL BINDING PROTEIN / isoprenoids / deoxyxylulose/methyl-erythritol-phosphate pathway / cyclodiphosphate / MEP / YgbB / ispF / MECDP / 2-C-methyl-D-erythritol-2 / 4-cyclodiphosphate synthase | ||||||
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 / ubiquinone biosynthetic process / isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway / terpenoid biosynthetic process / manganese ion binding / zinc ion binding / identical protein binding / metal ion binding Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Rigid body / Resolution: 2.8 Å | ||||||
Authors | Richard, S.B. / Ferrer, J.L. / Bowman, M.E. / Lillo, A.M. / Tetzlaff, C.N. / Cane, D.E. / Noel, J.P. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2002 Title: Structure and mechanism of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase. An enzyme in the mevalonate-independent isoprenoid biosynthetic pathway. Authors: Richard, S.B. / Ferrer, J.L. / Bowman, M.E. / Lillo, A.M. / Tetzlaff, C.N. / Cane, D.E. / Noel, J.P. #1: Journal: Nat.Struct.Biol. / Year: 2001 Title: Structure of 4-diphosphocytidyl-2-C-methylerythritol Synthetase Involved in Mevalonate-Independent Isoprenoid Biosynthesis Authors: Richard, S.B. / Bowman, M.E. / Kwiatkowski, W. / Kang, I. / Chow, C. / Lillo, A.M. / Cane, D.E. / Noel, J.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1knk.cif.gz | 43.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1knk.ent.gz | 30 KB | Display | PDB format |
PDBx/mmJSON format | 1knk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1knk_validation.pdf.gz | 428.2 KB | Display | wwPDB validaton report |
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Full document | 1knk_full_validation.pdf.gz | 431.6 KB | Display | |
Data in XML | 1knk_validation.xml.gz | 8.5 KB | Display | |
Data in CIF | 1knk_validation.cif.gz | 10.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kn/1knk ftp://data.pdbj.org/pub/pdb/validation_reports/kn/1knk | HTTPS FTP |
-Related structure data
Related structure data | 1knjSC S: Starting model for refinement C: citing same article (ref.) |
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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 on special symmetry positions |
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Details | The biological assembly is a homotrimer generated from the monomer in the asymmetric unit by the operations: z,x,y and y,z,x |
-Components
#1: Protein | Mass: 16920.531 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ispF / Plasmid: PHIS8 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P62617 |
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#2: Chemical | ChemComp-MN / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: (NH4)2SO4, PEG 400, NaI, PIPES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 4 ℃ | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9793 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 10, 2001 |
Radiation | Monochromator: Si(111) OR Si(311) CRYSTALS, LN2 COOLED / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→30 Å / Num. all: 24117 / Num. obs: 24117 / % possible obs: 93.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 0 / Redundancy: 3.54 % / Biso Wilson estimate: 111.6 Å2 / Rsym value: 0.091 / Net I/σ(I): 15.7 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 5 / Num. unique all: 404 / Rsym value: 0.415 / % possible all: 96.9 |
Reflection | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 99 Å / Num. obs: 11929 / Redundancy: 3.55 % / Num. measured all: 41619 / Rmerge(I) obs: 0.091 |
Reflection shell | *PLUS % possible obs: 96.9 % / Rmerge(I) obs: 0.415 |
-Processing
Software |
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Refinement | Method to determine structure: Rigid body Starting model: PDB ENTRY 1KNJ Resolution: 2.8→24.74 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 623227.17 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 58.3984 Å2 / ksol: 0.369238 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 72.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.8→24.74 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.98 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS % reflection Rfree: 5 % / Rfactor Rfree: 0.253 / Rfactor Rwork: 0.243 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.367 / Rfactor Rwork: 0.366 |