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- PDB-1w56: 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: 1w56 | ||||||
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Title | Stepwise introduction of zinc binding site into porphobilinogen synthase of Pseudomonas aeruginosa (mutations A129C and D131C) | ||||||
![]() | 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 | ![]() | 165.4 KB | Display | ![]() |
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PDB format | ![]() | 131.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 390.6 KB | Display | ![]() |
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Full document | ![]() | 399.1 KB | Display | |
Data in XML | ![]() | 15.3 KB | Display | |
Data in CIF | ![]() | 27.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1w54C ![]() 1w5mC ![]() 1w5nC ![]() 1w5oC ![]() 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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.83458, 0.55086, 0.00503), Vector: |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 37084.020 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, 702 molecules ![](data/chem/img/FMT.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/K.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/K.gif)
![](data/chem/img/HOH.gif)
#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 129, ALA TURNED INTO CYS AND POSITION 131, ASP TURNED INTO CYS. ...AMINO ACID EXCHANGE IN POSITION 129, ALA TURNED INTO CYS AND POSITION 131, ASP TURNED INTO CYS. FORMIC ACID IS USED TO REPRESENT CARBOXYLIC |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 45.07 % |
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 7.5 Details: HANGING DROP. DROPS WERE MIXED OF 5 MICROLITER OF PROTEIN SOLUTION (9 MG/ML PROTEIN, 50 MM NA-HEPES PH 7.5, 10MM MGCL2, 10MM ZNCL2, 10 MM DTT) PLUS 5 MICROLITER OF RESERVOIR SOLUTION (31.5 % ...Details: HANGING DROP. DROPS WERE MIXED OF 5 MICROLITER OF PROTEIN SOLUTION (9 MG/ML PROTEIN, 50 MM NA-HEPES PH 7.5, 10MM MGCL2, 10MM ZNCL2, 10 MM DTT) PLUS 5 MICROLITER OF RESERVOIR SOLUTION (31.5 % (W/V) PEG 400, 100MM NA-HEPES PH 7.5, 20 MM MGCL2, 20MM BETA-MERCAPTOETHANOLE) ON GLASS COVER SLIDES,HANGING ABOVE 500 MICROLITER OF RESERVOIR SOLUTION. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 20, 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: 1.7→20 Å / Num. obs: 75220 / % possible obs: 98.5 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 17.8 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 3.2 / % possible all: 98 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1B4K Resolution: 1.7→87.71 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.605 / SU ML: 0.053 / Cross valid method: THROUGHOUT / ESU R: 0.087 / ESU R Free: 0.093 / 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: 18.92 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→87.71 Å
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Refine LS restraints |
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