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Yorodumi- PDB-1w5o: Stepwise introduction of zinc binding site into porphobilinogen s... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1w5o | ||||||
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Title | Stepwise introduction of zinc binding site into porphobilinogen synthase of Pseudomonas aeruginosa (mutations A129C, D131C and 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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 | 1w5o.cif.gz | 160.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1w5o.ent.gz | 126.5 KB | Display | PDB format |
PDBx/mmJSON format | 1w5o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w5/1w5o ftp://data.pdbj.org/pub/pdb/validation_reports/w5/1w5o | HTTPS FTP |
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-Related structure data
Related structure data | 1w54C 1w56C 1w5mC 1w5nC 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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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.81575, 0.57837, 0.00609), Vector: |
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 37072.074 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Strain: PAO1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q59643, porphobilinogen synthase |
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-Non-polymers , 5 types, 662 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 | ACCIDENTAL POINT MUTATION IN THE ORIGINAL GENE CAUSES I199V, THREE ADDITIONAL ENGINEERED MUTATIONS ...ACCIDENTAL |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.49 % |
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Crystal grow | Method: vapor diffusion, sitting drop / pH: 6 Details: SITTING DROP. DROPS WERE MIXED OF 3 MICROLITER OF PROTEIN SOLUTION (7 MG/ML PROTEIN, 50 MM NA-HEPES PH 7.5, 10MM MGCL2, 10MM ZNCL2, 10 MM DTT) PLUS 3 MICROLITER OF RESERVOIR SOLUTION (1M ...Details: SITTING DROP. DROPS WERE MIXED OF 3 MICROLITER OF PROTEIN SOLUTION (7 MG/ML PROTEIN, 50 MM NA-HEPES PH 7.5, 10MM MGCL2, 10MM ZNCL2, 10 MM DTT) PLUS 3 MICROLITER OF RESERVOIR SOLUTION (1M K/NA-TARTRATE, 100MM MES PH 6.0, 20MM BETA-MERCAPTOETHANOLE), 100 MICROLITER OF RESERVOIR SOLUTION, 96 WELL PLATES (NUNC) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 18, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.05 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→20 Å / Num. obs: 59936 / % possible obs: 99.9 % / Redundancy: 14.3 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 29.6 |
Reflection shell | Resolution: 1.85→1.88 Å / Redundancy: 14.6 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 9.3 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1B4K Resolution: 1.85→91.29 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.952 / SU ML: 0.06 / Cross valid method: THROUGHOUT / ESU R: 0.106 / ESU R Free: 0.107 / 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: 20.09 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→91.29 Å
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Refine LS restraints |
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