[English] 日本語
Yorodumi- PDB-1inj: CRYSTAL STRUCTURE OF THE APO FORM OF 4-DIPHOSPHOCYTIDYL-2-C-METHY... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1inj | ||||||
---|---|---|---|---|---|---|---|
Title | CRYSTAL STRUCTURE OF THE APO FORM OF 4-DIPHOSPHOCYTIDYL-2-C-METHYLERYTHRITOL (CDP-ME) SYNTHETASE (YGBP) INVOLVED IN MEVALONATE INDEPENDENT ISOPRENOID BIOSYNTHESIS | ||||||
Components | 4-DIPHOSPHOCYTIDYL-2-C-METHYLERYTHRITOL SYNTHETASE | ||||||
Keywords | TRANSFERASE / YGBP / CYTIDYLYLTRANSFERASE / DEOXYXYLULOSE-5-PHOSPHATE PATHWAY (DXP) / ISOPRENOID BIOSYNTHESIS / APO FORM | ||||||
Function / homology | Function and homology information 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase / 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase activity / isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway / terpenoid biosynthetic process / magnesium ion binding / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.55 Å | ||||||
Authors | Richard, S.B. / Bowman, M.E. / Kwiatkowski, W. / Kang, I. / Chow, C. / Lillo, A. / Cane, D.E. / Noel, J.P. | ||||||
Citation | 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 | 1inj.cif.gz | 64.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1inj.ent.gz | 45.6 KB | Display | PDB format |
PDBx/mmJSON format | 1inj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/in/1inj ftp://data.pdbj.org/pub/pdb/validation_reports/in/1inj | HTTPS FTP |
---|
-Related structure data
Related structure data | 1i52SC 1iniC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 25772.266 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: ISPD / Plasmid: PHIS8 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: Q46893, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases |
---|---|
#2: Chemical | ChemComp-CA / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.92 % | |||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 279 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG 8000, CALCIUM ACETATE, MAGNESIUM CHLORIDE, DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 279K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1.08 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 6, 2000 / Details: double crystal monochromator |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→90 Å / Num. all: 33935 / Num. obs: 30652 / % possible obs: 90.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.2 % / Biso Wilson estimate: 22.2 Å2 / Rsym value: 2.6 / Net I/σ(I): 32.7 |
Reflection shell | Resolution: 1.55→1.58 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.268 / Num. unique all: 880 / Rsym value: 26.8 / % possible all: 51.8 |
Reflection | *PLUS Rmerge(I) obs: 0.026 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 1I52 Resolution: 1.55→33.93 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1135780.99 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 1135780.99 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 43.79 Å2 / ksol: 0.3589 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.6 Å2
| ||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.55→33.93 Å
| ||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.55→1.65 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS % reflection Rfree: 5.1 % | ||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 27.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
| ||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.321 / % reflection Rfree: 5.1 % / Rfactor Rwork: 0.304 |