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Yorodumi- PDB-1w54: Stepwise introduction of a zinc binding site into Porphobilinogen... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1w54 | ||||||
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Title | Stepwise introduction of a zinc binding site into Porphobilinogen synthase from Pseudomonas aeruginosa (mutation D139C) | ||||||
Components | DELTA-AMINOLEVULINIC ACID DEHYDRATASE | ||||||
Keywords | SYNTHASE / EVOLUTION / METALLOENZYME / PORPHOBILINOGEN SYNTHASE / PSEUDOMONAS AERUGINOSA / PROTEIN ENGINEERING | ||||||
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: 2.2 Å | ||||||
Authors | Frere, F. / Reents, H. / Schubert, W.-D. / Heinz, D.W. / Jahn, D. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2005 Title: Tracking the Evolution of Porphobilinogen Synthase Metal Dependence in Vitro Authors: Frere, F. / Reents, H. / Schubert, W.-D. / Heinz, D.W. / Jahn, D. | ||||||
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 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 | 1w54.cif.gz | 144.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1w54.ent.gz | 112.9 KB | Display | PDB format |
PDBx/mmJSON format | 1w54.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w5/1w54 ftp://data.pdbj.org/pub/pdb/validation_reports/w5/1w54 | HTTPS FTP |
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-Related structure data
Related structure data | 1w56C 1w5mC 1w5nC 1w5oC 1w5pC 1w5qC 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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.84395, 0.53629, 0.0122), Vector: |
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 37051.953 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 , 5 types, 312 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Compound details | CATALYTIC ACTIVITY: 2 5-AMINOLEVULINATE = PORPHOBILINOGEN + 2 H(2)O. ENGINEERED MUTATION IN CHAINS ...CATALYTIC ACTIVITY: 2 5-AMINOLEVUL |
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Sequence details | AMINO ACID EXCHANGE IN POSITION 139, ASP TURNED INTO CYS FORMIC ACID IS USED TO REPRESENT ...AMINO ACID EXCHANGE IN POSITION 139, ASP TURNED INTO CYS FORMIC ACID IS USED TO REPRESENT CARBOXYLIC |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.38 % |
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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 (8,7 MG/ML PROTEIN, 50 MM NA-HEPES PH 7.5, 10 MM MGCL2, 10 ZNCL2, 10 MM DTT) PLUS 5 MICROL RESERVOIR SOLUTION ...Details: HANGING DROP IN 24-WELL LIMBRO PLATES. DROPS MADE OF 5 MICROL PROTEIN SOLUTION (8,7 MG/ML PROTEIN, 50 MM NA-HEPES PH 7.5, 10 MM MGCL2, 10 ZNCL2, 10 MM DTT) PLUS 5 MICROL RESERVOIR SOLUTION (28,5 % (W/V) PEG-400, 100 MM NA-HEPES PH 7.5, 80MM MGCL2, 20MM DTT) ABOVE 500 MICROL OF RESERVOIR SOLUTION. |
-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 R-AXIS IV / Detector: IMAGE PLATE / Date: Mar 15, 2002 / 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: 2.2→47.1 Å / Num. obs: 35228 / % possible obs: 99.8 % / Redundancy: 12.6 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 23.1 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 11.8 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 5.3 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1B4K Resolution: 2.2→87.71 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.928 / SU B: 4.622 / SU ML: 0.12 / Cross valid method: THROUGHOUT / ESU R: 0.227 / ESU R Free: 0.194 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.84 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→87.71 Å
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Refine LS restraints |
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