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Yorodumi- PDB-2c19: 5-(4-Carboxy-2-oxo-butylsulfanyl)-4-oxo-pentanoic acid acid bound... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2c19 | ||||||
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Title | 5-(4-Carboxy-2-oxo-butylsulfanyl)-4-oxo-pentanoic acid 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: 2.05 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 BA" IN EACH CHAIN ON SHEET RECORDS ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA BA" IN EACH CHAIN ON SHEET RECORDS BELOW ARE ACTUALLY 11-STRANDED BARRELS THIS ARE REPRESENTED BY 12-STRANDED SHEETS 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 | 2c19.cif.gz | 164.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2c19.ent.gz | 131.1 KB | Display | PDB format |
PDBx/mmJSON format | 2c19.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2c19_validation.pdf.gz | 443.3 KB | Display | wwPDB validaton report |
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Full document | 2c19_full_validation.pdf.gz | 453.1 KB | Display | |
Data in XML | 2c19_validation.xml.gz | 33.7 KB | Display | |
Data in CIF | 2c19_validation.cif.gz | 51.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c1/2c19 ftp://data.pdbj.org/pub/pdb/validation_reports/c1/2c19 | HTTPS FTP |
-Related structure data
Related structure data | 2c13C 2c14C 2c15C 2c16C 2c18C 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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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.81813, 0.57501, 0.00498), Vector: |
-Components
#1: Protein | Mass: 37291.152 Da / Num. of mol.: 2 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 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Sequence 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: 46.7 % |
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 7.5 Details: HANGING DROP IN 24-WELL LIMBRO PLATES. DROPS MADE OF 5 MICROL PROTEIN SOLUTION (10 MG/ML PROTEIN, 50 MM TRIS-HCL, PH 7.5, 5 MM MGCL2, 10 MM 5-(4-CARBOXY-2-OXO-BUTYLSULFANYL)-4-OXO-PENTANOIC ...Details: HANGING DROP IN 24-WELL LIMBRO PLATES. DROPS MADE OF 5 MICROL PROTEIN SOLUTION (10 MG/ML PROTEIN, 50 MM TRIS-HCL, PH 7.5, 5 MM MGCL2, 10 MM 5-(4-CARBOXY-2-OXO-BUTYLSULFANYL)-4-OXO-PENTANOIC ACID DISODIUM SALT) PLUS 5 MICROL RESERVOIR SOLUTION (17.0 % (W/V) PEG-3350, 120 MM NA-TARTRATE) ABOVE 500 MICROL OF RESERVOIR SOLUTION. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Wavelength: 1.5418 |
Detector | Type: RIGAKU R-AXIS IV / Detector: IMAGE PLATE / Date: Jan 14, 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: 2.05→34.26 Å / Num. obs: 44731 / % possible obs: 97.8 % / Redundancy: 10.5 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 14.5 |
Reflection shell | Resolution: 2.05→2.1 Å / Redundancy: 9.5 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 0.04 / % possible all: 97.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1B4K Resolution: 2.05→89.8 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.936 / SU B: 3.499 / SU ML: 0.097 / Cross valid method: THROUGHOUT / ESU R: 0.187 / ESU R Free: 0.164 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 5-(4-CARBOXY-2-OXO-BUTYLSULFANYL)-4-OXO- PENTANOIC ACID WAS INITIALLY BOUND TO K 205 AND K260 VIA SCHIFF BASES. A ALDOLE ADDITION RESULTED ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 5-(4-CARBOXY-2-OXO-BUTYLSULFANYL)-4-OXO- PENTANOIC ACID WAS INITIALLY BOUND TO K 205 AND K260 VIA SCHIFF BASES. A ALDOLE ADDITION RESULTED IN THE MODIFIED RESIDUE IN POSITION 205 THAT IS ADDITIONALLY BOUND TO THE AMINO MOIETY OF K260 VIA A SINGLE BOND.
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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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.43 Å2
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Refinement step | Cycle: LAST / Resolution: 2.05→89.8 Å
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