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Yorodumi- PDB-1l6s: Crystal Structure of Porphobilinogen Synthase Complexed with the ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1l6s | ||||||
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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 / DEHYDRATASE | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Jaffe, E.K. / Kervinen, J. / Martins, J. / Stauffer, F. / Neier, R. / Wlodawer, A. / Zdanov, A. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2002 Title: Species-Specific Inhibition of Porphobilinogen Synthase by 4-Oxosebacic Acid Authors: Jaffe, E.K. / Kervinen, J. / Martins, J. / Stauffer, F. / Neier, R. / Wlodawer, A. / Zdanov, A. #1: 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 | 1l6s.cif.gz | 148.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1l6s.ent.gz | 115.9 KB | Display | PDB format |
PDBx/mmJSON format | 1l6s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l6/1l6s ftp://data.pdbj.org/pub/pdb/validation_reports/l6/1l6s | HTTPS FTP |
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-Related structure data
Related structure data | 1l6yC 1i8jS 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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Details | The biological assembly is an octamer |
-Components
#1: Protein | Mass: 35613.727 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 / | |
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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: 4.17 Å3/Da / Density % sol: 70.5 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG 3350, 10% GLYCEROL, 0.1M TRIS-HCL, PH 8.5, 0.02% SODIUM AZIDE, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8.5 / 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: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 1.28 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 18, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.28 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→40 Å / Num. all: 131991 / Num. obs: 126253 / % possible obs: 95.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.056 |
Reflection shell | Resolution: 1.7→1.76 Å / Rmerge(I) obs: 0.287 / Mean I/σ(I) obs: 2.3 / Num. unique all: 9036 / % possible all: 69.6 |
Reflection | *PLUS Lowest resolution: 40 Å / Rmerge(I) obs: 0.051 |
Reflection shell | *PLUS Rmerge(I) obs: 0.287 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1I8J Resolution: 1.7→40 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.7→40 Å
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Refine LS restraints |
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Refinement | *PLUS Lowest resolution: 40 Å / Rfactor obs: 0.195 / Rfactor Rfree: 0.243 / Rfactor Rwork: 0.195 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS |