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Yorodumi- PDB-1nfz: STRUCTURE AND MECHANISM OF ACTION OF ISOPENTENYLPYROPHOSPHATE-DIM... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1nfz | ||||||
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Title | STRUCTURE AND MECHANISM OF ACTION OF ISOPENTENYLPYROPHOSPHATE-DIMETHYLALLYLPYROPHOSPHATE 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 / MOLECULAR REPLACEMENT / Resolution: 1.97 Å | ||||||
Authors | Wouters, J. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2003 Title: Catalytic Mechanism of Escherichia coli Isopentenyl Diphosphate Isomerase Involves Cys-67, Glu-116, and Tyr-104 as Suggested by Crystal Structures of Complexes with Transition State Analogues ...Title: Catalytic Mechanism of Escherichia coli Isopentenyl Diphosphate Isomerase Involves Cys-67, Glu-116, and Tyr-104 as Suggested by Crystal Structures of Complexes with Transition State Analogues and Irreversible Inhibitors Authors: Wouters, J. / Oudjama, Y. / Barkley, S.J. / Tricot, C. / Stalon, V. / Droogmans, L. / Poulter, C.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1nfz.cif.gz | 92 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1nfz.ent.gz | 67.7 KB | Display | PDB format |
PDBx/mmJSON format | 1nfz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1nfz_validation.pdf.gz | 965.6 KB | Display | wwPDB validaton report |
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Full document | 1nfz_full_validation.pdf.gz | 994.6 KB | Display | |
Data in XML | 1nfz_validation.xml.gz | 19.5 KB | Display | |
Data in CIF | 1nfz_validation.cif.gz | 27.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nf/1nfz ftp://data.pdbj.org/pub/pdb/validation_reports/nf/1nfz | HTTPS FTP |
-Related structure data
Related structure data | 1nfsC 1hztS S: Starting model for refinement C: citing same article (ref.) |
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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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-Components
#1: Protein | Mass: 20644.391 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / 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: 2.58 Å3/Da / Density % sol: 52 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 5.5 Details: PEG 2000, MANGANESE CHLORIDE, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 100K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||
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: IMAGING PLATE / 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: 1.97→10 Å / Num. all: 28408 / Num. obs: 26786 / % possible obs: 98.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 4 / Rmerge(I) obs: 0.037 / Net I/σ(I): 8.8 |
Reflection shell | Resolution: 1.97→2.08 Å / Rmerge(I) obs: 0.101 / Mean I/σ(I) obs: 5.1 / % possible all: 97.2 |
Reflection | *PLUS Num. measured all: 102886 |
Reflection shell | *PLUS % possible obs: 97.2 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1HZT Resolution: 1.97→10 Å / Num. parameters: 12891 / Num. restraintsaints: 15405 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
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Refine analyze | Num. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 3222 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.97→10 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL / Version: 97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 10 Å / % reflection Rfree: 10 % / Rfactor obs: 0.18 / Rfactor Rwork: 0.176 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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