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- PDB-1w5o: Stepwise introduction of zinc binding site into porphobilinogen s... -
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Open data
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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) | ||||||
![]() | DELTA-AMINOLEVULINIC ACID DEHYDRATASE | ||||||
![]() | SYNTHASE / EVOLUTION / METALLOENZYME / PORPHOBILINOGEN SYNTHASE / PSEUDOMONAS AERUGINOSA / PROTEIN ENGINEERING | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Frere, F. / Reents, H. / Schubert, W.-D. / Heinz, D.W. / Jahn, D. | ||||||
![]() | ![]() 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. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 160.2 KB | Display | ![]() |
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PDB format | ![]() | 126.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | 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 ( |
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Similar structure data |
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Links
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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: |
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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.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 662 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/K.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/K.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/ZN.gif)
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#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: ![]() |
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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: ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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