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Open data
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Basic information
Entry | Database: PDB / ID: 2g73 | ||||||
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Title | Y104F mutant type 1 IPP isomerase complex with EIPP | ||||||
![]() | Isopentenyl-diphosphate delta-isomerase | ||||||
![]() | ISOMERASE / COMPLEX | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | de Ruyck, J. / Wouters, J. | ||||||
![]() | ![]() 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. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 88.2 KB | Display | ![]() |
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PDB format | ![]() | 65.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
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Full document | ![]() | 1.5 MB | Display | |
Data in XML | ![]() | 11.9 KB | Display | |
Data in CIF | ![]() | 16.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1r67C ![]() 2b2kC ![]() 2g74C ![]() 1hx3S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 20628.391 Da / Num. of mol.: 2 / Mutation: Y104F Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q46822, isopentenyl-diphosphate Delta-isomerase #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.74 Å3/Da / Density % sol: 55.18 % |
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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 |
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Diffraction source | Source: ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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
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Refine analyze | Num. disordered residues: 2 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 2969 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.97→10 Å
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Refine LS restraints |
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