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- PDB-4c5w: Three dimensional structure of human gamma-butyrobetaine hydroxyl... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4c5w | ||||||
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Title | Three dimensional structure of human gamma-butyrobetaine hydroxylase in complex with 4-(Ethyldimethylammonio)butanoate | ||||||
![]() | GAMMA-BUTYROBETAINE DIOXYGENASE | ||||||
![]() | OXIDOREDUCTASE | ||||||
Function / homology | ![]() gamma-butyrobetaine dioxygenase / gamma-butyrobetaine dioxygenase activity / Carnitine synthesis / carnitine biosynthetic process / iron ion binding / mitochondrion / zinc ion binding / extracellular exosome / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Tars, K. / Leitans, J. / Kazaks, A. | ||||||
![]() | ![]() Title: Targeting Carnitine Biosynthesis: Discovery of New Inhibitors Against Gamma-Butyrobetaine Hydroxylase. Authors: Tars, K. / Leitans, J. / Kazaks, A. / Zelencova, D. / Liepinsh, E. / Kuka, J. / Makrecka, M. / Lola, D. / Andrianovs, V. / Gustina, D. / Grinberga, S. / Liepinsh, E. / Kalvinsh, I. / ...Authors: Tars, K. / Leitans, J. / Kazaks, A. / Zelencova, D. / Liepinsh, E. / Kuka, J. / Makrecka, M. / Lola, D. / Andrianovs, V. / Gustina, D. / Grinberga, S. / Liepinsh, E. / Kalvinsh, I. / Dambrova, M. / Loza, E. / Pugovics, O. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 105.3 KB | Display | ![]() |
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PDB format | ![]() | 78.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 453.3 KB | Display | ![]() |
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Full document | ![]() | 453.2 KB | Display | |
Data in XML | ![]() | 19.9 KB | Display | |
Data in CIF | ![]() | 30.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4bg1C ![]() 4bgkC ![]() 4bgmC ![]() 4bhfC ![]() 4bhiC ![]() 3o2gS 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
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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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 44774.867 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: O75936, gamma-butyrobetaine dioxygenase |
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-Non-polymers , 5 types, 417 molecules ![](data/chem/img/OGA.gif)
![](data/chem/img/NM3.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/16D.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NM3.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/16D.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-OGA / | ||||
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#3: Chemical | ChemComp-NM3 / | ||||
#4: Chemical | ChemComp-ZN / #5: Chemical | ChemComp-16D / | #6: Water | ChemComp-HOH / | |
-Details
Nonpolymer details | 4-(ETHYLDIMETHYLAMMONIO)BUTANOATE (NM3): ONE METHYL GROUP IS NOT SHOWN IN ATOMIC COORDINATE FILE ...4-(ETHYLDIMET |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 52 % / Description: NONE |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 15 % PEG 3350, 1 % 1.6-DIAMINOHEXANE, 200 MM AMMONIUM CITRATE PH 7.0, 10 MM ZNSO4, 8 MM N-OXALYLGLYCINE, 4 MM INHIBITOR, PROTEIN 6.5 MG/ML, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K, TIME 2-7 DAYS |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Feb 1, 2013 / Details: MIRRORS |
Radiation | Monochromator: DOUBLE SI CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→28.95 Å / Num. obs: 50058 / % possible obs: 100 % / Redundancy: 3.7 % / Biso Wilson estimate: 17.633 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 9.1 |
Reflection shell | Resolution: 1.7→1.79 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 2.1 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3O2G Resolution: 1.7→28.85 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.955 / SU B: 2.127 / SU ML: 0.068 / Cross valid method: THROUGHOUT / ESU R: 0.094 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.581 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→28.85 Å
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Refine LS restraints |
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