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Yorodumi- PDB-2c13: 5-hydroxy-levulinic acid bound to Porphobilinogen synthase from P... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2c13 | ||||||
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Title | 5-hydroxy-levulinic acid bound to Porphobilinogen synthase from Pseudomonas aeruginosa | ||||||
Components | DELTA-AMINOLEVULINIC ACID DEHYDRATASE | ||||||
Keywords | LYASE / ENZYME MECHANISM / METALLOENZYME / PORPHOBILINOGEN SYNTHASE / COCRYSTALLIZATION / PORPHYRIN BIOSYNTHESIS | ||||||
Function / homology | Function and homology information porphobilinogen synthase / porphobilinogen synthase activity / porphyrin-containing compound biosynthetic process / protoporphyrinogen IX biosynthetic process / heme biosynthetic process / zinc ion binding / cytosol Similarity search - Function | ||||||
Biological species | PSEUDOMONAS AERUGINOSA (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | ||||||
Authors | Frere, F. / Nentwich, M. / Gacond, S. / Heinz, D.W. / Neier, R. / Frankenberg-Dinkel, N. | ||||||
Citation | Journal: Biochemistry / Year: 2006 Title: Probing the Active Site of Pseudomonas Aeruginosa Porphobilinogen Synthase Using Newly Developed Inhibitors. Authors: Frere, F. / Nentwich, M. / Gacond, S. / Heinz, D.W. / Neier, R. / Frankenberg-Dinkel, N. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 11-STRANDED BARREL THIS IS REPRESENTED BY A 12-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 11-STRANDED BARREL THIS IS REPRESENTED BY A 12-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2c13.cif.gz | 160.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2c13.ent.gz | 127.3 KB | Display | PDB format |
PDBx/mmJSON format | 2c13.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c1/2c13 ftp://data.pdbj.org/pub/pdb/validation_reports/c1/2c13 | HTTPS FTP |
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-Related structure data
Related structure data | 2c14C 2c15C 2c16C 2c18C 2c19C 1b4kS 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 on special symmetry positions |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 37290.078 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q59643, porphobilinogen synthase |
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-Non-polymers , 6 types, 466 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-PEG / | #5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Details
Compound details | ENGINEEREDSequence details | I199V EXCHANGE AS CLONING ARTEFACT | |
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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: 2.3 Å3/Da / Density % sol: 45.4 % |
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 7 Details: HANGING DROP IN 24-WELL LIMBRO PLATES.DROPS MADE OF 5 MICROL PROTEIN SOLUTION (10 MG/ML PROTEIN, 0.05 M TRIS-HCL, PH 7.5, 0.005 M MGCL2, 0.01 M 5-OH-4-OXO-PENTANOIC ACID SODIUM SALT PLUS 5 ...Details: HANGING DROP IN 24-WELL LIMBRO PLATES.DROPS MADE OF 5 MICROL PROTEIN SOLUTION (10 MG/ML PROTEIN, 0.05 M TRIS-HCL, PH 7.5, 0.005 M MGCL2, 0.01 M 5-OH-4-OXO-PENTANOIC ACID SODIUM SALT PLUS 5 MICROL RESERVOIR SOLUTION 9.0 % (W/V) PEG-4000, 0.180 M KCL, 0.009 M CACL2, 0.05 M NA-CACODYLATE PH 6.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 |
Detector | Type: RIGAKU-MSC R-AXIS IV / Detector: IMAGE PLATE / Date: Jan 31, 2005 / Details: BLUE OPTIC |
Radiation | Monochromator: OSMIC CONFOCAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→40.2 Å / Num. obs: 37881 / % possible obs: 99.5 % / Redundancy: 11 % / Biso Wilson estimate: 22.5 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 16.7 |
Reflection shell | Resolution: 2.15→2.23 Å / Redundancy: 9.9 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 4.9 / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1B4K Resolution: 2.15→89.8 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.929 / SU B: 4.213 / SU ML: 0.112 / Cross valid method: THROUGHOUT / ESU R: 0.238 / ESU R Free: 0.183 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.69 Å2
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Refinement step | Cycle: LAST / Resolution: 2.15→89.8 Å
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Refine LS restraints |
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