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Yorodumi- PDB-1i8j: CRYSTAL STRUCTURE OF PORPHOBILINOGEN SYNTHASE COMPLEXED WITH THE ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1i8j | ||||||
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Title | CRYSTAL STRUCTURE OF PORPHOBILINOGEN SYNTHASE COMPLEXED WITH THE INHIBITOR 4,7-DIOXOSEBACIC ACID | ||||||
Components | PORPHOBILINOGEN SYNTHASEDelta-aminolevulinic acid dehydratase | ||||||
Keywords | LYASE / HEME BIOSYNTHESIS / MAGNESIUM / 4 / 7-DIOXOSEBACIC ACID | ||||||
Function / homology | Function and homology information porphobilinogen synthase / porphobilinogen synthase activity / protoporphyrinogen IX biosynthetic process / heme biosynthetic process / magnesium ion binding / zinc ion binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Kervinen, J. / Jaffe, E.K. / Stauffer, F. / Neier, R. / Wlodawer, A. / Zdanov, A. | ||||||
Citation | Journal: Biochemistry / Year: 2001 Title: Mechanistic basis for suicide inactivation of porphobilinogen synthase by 4,7-dioxosebacic acid, an inhibitor that shows dramatic species selectivity. Authors: Kervinen, J. / Jaffe, E.K. / Stauffer, F. / Neier, R. / Wlodawer, A. / Zdanov, A. | ||||||
History |
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Remark 600 | HETEROGEN Atoms C4 and C7 of DSB form a Schiff base to NZ of Lys246 and NZ of Lys194. The oxygens ...HETEROGEN Atoms C4 and C7 of DSB form a Schiff base to NZ of Lys246 and NZ of Lys194. The oxygens on the C4 and C7 are eliminated during this reaction. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1i8j.cif.gz | 142.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1i8j.ent.gz | 111.4 KB | Display | PDB format |
PDBx/mmJSON format | 1i8j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i8/1i8j ftp://data.pdbj.org/pub/pdb/validation_reports/i8/1i8j | HTTPS FTP |
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-Related structure data
Related structure data | 1b4eS 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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-Components
#1: Protein | Mass: 35537.609 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: P0ACB2, porphobilinogen synthase #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Nonpolymer details | ATOMS C4 AND C7 OF DSB FORM A SCHIFF BASE TO NZ OF LYS246 AND NZ OF LYS194. THE OXYGENS ON THE C4 ...ATOMS C4 AND C7 OF DSB FORM A SCHIFF BASE TO NZ OF LYS246 AND NZ OF LYS194. THE OXYGENS ON THE C4 AND C7 ARE ELIMINATED | |
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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: 4.16 Å3/Da / Density % sol: 70.43 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: PEG 3350, GLYCEROL, TRIS-HCL, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 10, 2000 / Details: OSMIC |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→35 Å / Num. all: 94638 / Num. obs: 94536 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 5.6 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 12 |
Reflection shell | Resolution: 1.9→1.93 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.5 / % possible all: 99.8 |
Reflection | *PLUS Lowest resolution: 35 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1b4e Resolution: 1.9→35 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.9→35 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 35 Å / σ(F): 0 / Rfactor obs: 0.198 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS |