[English] 日本語
Yorodumi- PDB-1knj: Co-Crystal Structure of 2-C-methyl-D-erythritol 2,4-cyclodiphosph... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1knj | ||||||
---|---|---|---|---|---|---|---|
Title | Co-Crystal Structure of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate Synthase (ispF) from E. coli Involved in Mevalonate-Independent Isoprenoid Biosynthesis, Complexed with CMP/MECDP/Mn2+ | ||||||
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 / isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway / terpenoid biosynthetic process / ubiquinone 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 / MAD / 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1knj.cif.gz | 40.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1knj.ent.gz | 32.2 KB | Display | PDB format |
PDBx/mmJSON format | 1knj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1knj_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1knj_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 1knj_validation.xml.gz | 9.5 KB | Display | |
Data in CIF | 1knj_validation.cif.gz | 11.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kn/1knj ftp://data.pdbj.org/pub/pdb/validation_reports/kn/1knj | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
Unit cell |
| |||||||||
Components on special symmetry positions |
| |||||||||
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: 17108.113 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 |
---|---|
#2: Chemical | ChemComp-MN / |
#3: Chemical | ChemComp-C5P / |
#4: Chemical | ChemComp-CDI / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-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 | ||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | *PLUS Temperature: 4 ℃ | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction |
| ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source |
| ||||||||||||||||||
Detector | Type: MARRESEARCH / Detector: CCD / Date: Mar 26, 2001 / Details: mirrors | ||||||||||||||||||
Radiation |
| ||||||||||||||||||
Radiation wavelength |
| ||||||||||||||||||
Reflection | Resolution: 2.7→99 Å / Num. all: 11923 / Num. obs: 11923 / % possible obs: 99.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.1 % / Biso Wilson estimate: 92 Å2 / Rmerge(I) obs: 0.04 / Rsym value: 0.066 / Net I/σ(I): 19 | ||||||||||||||||||
Reflection shell | Resolution: 2.8→2.87 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 482 / Num. unique all: 1579 / % possible all: 100 | ||||||||||||||||||
Reflection | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 99 Å / Num. obs: 24118 / Num. measured all: 96785 / Rmerge(I) obs: 0.066 | ||||||||||||||||||
Reflection shell | *PLUS % possible obs: 100 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 1.2 |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MAD / Resolution: 2.8→14.71 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 1949090.32 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 41.9833 Å2 / ksol: 0.333926 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 62.6 Å2
| |||||||||||||||||||||||||
Refine analyze |
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→14.71 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
LS refinement shell | Resolution: 2.8→2.98 Å / Rfactor Rfree error: 0.038 / Total num. of bins used: 6
| |||||||||||||||||||||||||
Xplor file |
| |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.8 Å / % reflection Rfree: 5 % / Rfactor all: 0.286 / Rfactor Rfree: 0.258 / Rfactor Rwork: 0.23 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
| |||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.37 / Rfactor Rwork: 0.334 |