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Yorodumi- PDB-1q54: STRUCTURE AND MECHANISM OF ACTION OF ISOPENTENYLPYROPHOSPHATE-DIM... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1q54 | |||||||||
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Title | STRUCTURE AND MECHANISM OF ACTION OF ISOPENTENYLPYROPHOSPHATE-DIMETHYLALLYLPYROPHOSPHATE ISOMERASE: COMPLEX WITH THE BROMOHYDRINE OF IPP | |||||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.93 Å | |||||||||
Authors | Wouters, J. / Oudjama, Y. / Ghosh, S. / Stalon, V. / Droogmans, L. | |||||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2003 Title: Structure and mechanism of action of isopentenylpyrophosphate-dimethylallylpyrophosphate isomerase. Authors: Wouters, J. / Oudjama, Y. / Ghosh, S. / Stalon, V. / Droogmans, L. / Oldfield, E. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1q54.cif.gz | 89.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1q54.ent.gz | 66.4 KB | Display | PDB format |
PDBx/mmJSON format | 1q54.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1q54_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 1q54_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 1q54_validation.xml.gz | 19.5 KB | Display | |
Data in CIF | 1q54_validation.cif.gz | 26.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q5/1q54 ftp://data.pdbj.org/pub/pdb/validation_reports/q5/1q54 | HTTPS FTP |
-Related structure data
Related structure data | 1hztS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological assembly corresponds to a dimer |
-Components
#1: Protein | Mass: 20612.324 Da / Num. of mol.: 2 / Mutation: C67A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PYL20 / Production host: Escherichia coli (E. coli) 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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.2 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: MnCl2, PEG2000, Ammonium Sulfate, pH 5.50, VAPOR DIFFUSION, HANGING DROP, temperature 297K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 5.5 / Method: vapor diffusion | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: ENRAF-NONIUS / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 1, 2000 / Details: mirrors |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.93→10 Å / Num. all: 29014 / Num. obs: 26583 / % possible obs: 95.1 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 4 / Redundancy: 2.6 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 6.2 |
Reflection shell | Resolution: 1.93→2.04 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.128 / Mean I/σ(I) obs: 4.7 / % possible all: 95 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1HZT Resolution: 1.93→10 Å / Num. parameters: 12257 / Num. restraintsaints: 15465 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
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Refine analyze | Num. disordered residues: 3 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 3029.63 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.93→10 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL / Version: 97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.21 / Rfactor Rfree: 0.2574 / Rfactor Rwork: 0.2014 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |