+Open data
-Basic information
Entry | Database: PDB / ID: 1r67 | ||||||
---|---|---|---|---|---|---|---|
Title | Y104A MUTANT OF E.COLI IPP ISOMERASE | ||||||
Components | Isopentenyl-diphosphate delta-isomeraseIsopentenyl-diphosphate delta isomerase | ||||||
Keywords | ISOMERASE / COMPLEX Y104A MUTANT | ||||||
Function / homology | Function and homology information isopentenyl-diphosphate Delta-isomerase / isopentenyl-diphosphate delta-isomerase activity / dimethylallyl diphosphate biosynthetic process / isoprenoid biosynthetic process / DNA damage response / magnesium ion binding / zinc ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å | ||||||
Authors | Wouters, J. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2006 Title: Structural role for Tyr-104 in Escherichia coli isopentenyl-diphosphate isomerase: site-directed mutagenesis, enzymology, and protein crystallography. Authors: de Ruyck, J. / Durisotti, V. / Oudjama, Y. / Wouters, J. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1r67.cif.gz | 48.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1r67.ent.gz | 32.6 KB | Display | PDB format |
PDBx/mmJSON format | 1r67.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r6/1r67 ftp://data.pdbj.org/pub/pdb/validation_reports/r6/1r67 | HTTPS FTP |
---|
-Related structure data
Related structure data | 2b2kC 2g73C 2g74C 1hztS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
Unit cell |
| |||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 21510.287 Da / Num. of mol.: 1 / Mutation: Y104A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: IDI OR B2889 / Production host: Escherichia coli (E. coli) References: UniProt: Q46822, isopentenyl-diphosphate Delta-isomerase |
---|---|
#2: Chemical | ChemComp-MG / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.99 Å3/Da / Density % sol: 41.75 % | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 275 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: PEG 2000, MANGANESE CHLORIDE, MAGNESIUM CHLORIDE, AMMONIUM SULFATE, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 275K | ||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion, hanging drop / PH range low: 6.5 / PH range high: 4.5 | ||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9292 / Wavelength: 0.9798 Å | |||||||||
Detector | Type: MARRESEARCH / Detector: CCD / Date: Apr 11, 2003 / Details: SI CRYSTALS | |||||||||
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
| |||||||||
Reflection | Resolution: 1.77→99 Å / Num. obs: 13869 / % possible obs: 89.9 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 4 / Rmerge(I) obs: 0.04 | |||||||||
Reflection shell | Resolution: 1.77→1.8 Å / Rmerge(I) obs: 0.161 / % possible all: 93.5 | |||||||||
Reflection | *PLUS Highest resolution: 1.76 Å / Num. obs: 16594 / Num. measured all: 31357 / Rmerge(I) obs: 0.04 | |||||||||
Reflection shell | *PLUS Highest resolution: 1.76 Å / % possible obs: 93.5 % / Rmerge(I) obs: 0.169 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1HZT Resolution: 1.77→8 Å / Num. parameters: 5368 / Num. restraintsaints: 5013 / Cross valid method: FREE R / σ(F): 4 / Stereochemistry target values: ENGH AND HUBER
| |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 1 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 1285.5 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.77→8 Å
| |||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||
Software | *PLUS Name: SHELXL / Version: 97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.76 Å / Lowest resolution: 10 Å / % reflection Rfree: 10 % / Rfactor all: 0.207 / Rfactor Rfree: 0.2356 / Rfactor Rwork: 0.19 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|