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- PDB-4v4d: Crystal Structure of Pyrogallol-Phloroglucinol Transhydroxylase f... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4v4d | |||||||||
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Title | Crystal Structure of Pyrogallol-Phloroglucinol Transhydroxylase from Pelobacter acidigallici complexed with pyrogallol | |||||||||
![]() | (Pyrogallol hydroxytransferase ...) x 2 | |||||||||
![]() | OXIDOREDUCTASE / Molybdenum binding enzyme / MGD-cofactors / DMSO-reductase family / 4Fe-4S-cluster / complex with substrate pyrogallol | |||||||||
Function / homology | ![]() pyrogallol hydroxytransferase / pyrogallol hydroxytransferase activity / molybdenum ion binding / molybdopterin cofactor binding / anaerobic respiration / outer membrane-bounded periplasmic space / 4 iron, 4 sulfur cluster binding / electron transfer activity / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Messerschmidt, A. / Niessen, H. / Abt, D. / Einsle, O. / Schink, B. / Kroneck, P.M.H. | |||||||||
![]() | ![]() Title: Crystal structure of pyrogallol-phloroglucinol transhydroxylase, an Mo enzyme capable of intermolecular hydroxyl transfer between phenols Authors: Messerschmidt, A. / Niessen, H. / Abt, D. / Einsle, O. / Schink, B. / Kroneck, P.M.H. | |||||||||
History |
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Remark 400 | THE COMPLETE CRYSTAL STRUCTURE IS REPRESENTED BY PDB STRUCTURES 1TI4 AND 1VLE |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 2.9 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4v4cC ![]() 4v4eC ![]() 1ti2 C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
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Components
-Pyrogallol hydroxytransferase ... , 2 types, 24 molecules ACEGIKMOQSUWBDFHJLNPRTVX
#1: Protein | Mass: 99379.898 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) ![]() #2: Protein | Mass: 31259.424 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) ![]() |
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-Non-polymers , 6 types, 10196 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/MGD.gif)
![](data/chem/img/4MO.gif)
![](data/chem/img/PYG.gif)
![](data/chem/img/SF4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MGD.gif)
![](data/chem/img/4MO.gif)
![](data/chem/img/PYG.gif)
![](data/chem/img/SF4.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-CA / #4: Chemical | ChemComp-MGD / #5: Chemical | ChemComp-4MO / #6: Chemical | ChemComp-PYG / #7: Chemical | ChemComp-SF4 / #8: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.71 Å3/Da / Density % sol: 55 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: PEG 8000, sodium acetate, potassium phosphate, sodium dithionite, sodium cacodylate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 4, 2002 / Details: mirror |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.05 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→25 Å / Num. all: 840476 / Num. obs: 814421 / % possible obs: 96.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.2 % / Biso Wilson estimate: 26.4 Å2 / Rmerge(I) obs: 0.14 / Rsym value: 0.14 / Net I/σ(I): 5.1 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.515 / Mean I/σ(I) obs: 1.4 / Rsym value: 0.515 / % possible all: 96.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1TI2 ![]() 1ti2 Resolution: 2.2→24.99 Å / Rfactor Rfree error: 0.001 / Data cutoff high absF: 4990834.44 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 50.5217 Å2 / ksol: 0.381544 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→24.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.002 / Total num. of bins used: 6
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Xplor file |
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