+Open data
-Basic information
Entry | Database: PDB / ID: 2g73 | ||||||
---|---|---|---|---|---|---|---|
Title | Y104F mutant type 1 IPP isomerase complex with EIPP | ||||||
Components | Isopentenyl-diphosphate delta-isomerase | ||||||
Keywords | ISOMERASE / COMPLEX | ||||||
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 / FOURIER SYNTHESIS / Resolution: 1.97 Å | ||||||
Authors | de Ruyck, J. / 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 | 2g73.cif.gz | 88.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2g73.ent.gz | 65.4 KB | Display | PDB format |
PDBx/mmJSON format | 2g73.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2g73_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2g73_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 2g73_validation.xml.gz | 11.9 KB | Display | |
Data in CIF | 2g73_validation.cif.gz | 16.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g7/2g73 ftp://data.pdbj.org/pub/pdb/validation_reports/g7/2g73 | HTTPS FTP |
-Related structure data
Related structure data | 1r67C 2b2kC 2g74C 1hx3S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 20628.391 Da / Num. of mol.: 2 / Mutation: Y104F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pET30b / Production host: Escherichia coli (E. coli) References: UniProt: Q46822, isopentenyl-diphosphate Delta-isomerase #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.74 Å3/Da / Density % sol: 55.18 % |
---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: PEG 2000 mme, MANGANESE AND MAGNESIUM CHLORIDE, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.54179 / Wavelength: 1.54179 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 30, 2005 / Details: MIRRORS |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54179 Å / Relative weight: 1 |
Reflection | Resolution: 1.97→10 Å / Num. all: 33019 / Num. obs: 28124 / % possible obs: 99.1 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 4 / Redundancy: 6.2 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 6.2 |
Reflection shell | Resolution: 1.97→2.03 Å / Rmerge(I) obs: 0.25 / % possible all: 92.4 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB entry 1HX3 Resolution: 1.97→10 Å / Num. parameters: 12001 / Num. restraintsaints: 11947 / Cross valid method: FREE R / σ(F): 4 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 2 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 2969 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.97→10 Å
| |||||||||||||||||||||||||||||||||
Refine LS restraints |
|