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Yorodumi- PDB-4bgm: Three dimensional structure of human gamma-butyrobetaine hydroxyl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4bgm | ||||||
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Title | Three dimensional structure of human gamma-butyrobetaine hydroxylase in complex with 3-Carboxy-N-(2-fluoroethyl)-N,N-dimethylpropan-1- aminium chloride | ||||||
Components | GAMMA-BUTYROBETAINE DIOXYGENASE | ||||||
Keywords | OXIDOREDUCTASE | ||||||
Function / homology | Function and homology information gamma-butyrobetaine dioxygenase / gamma-butyrobetaine dioxygenase activity / Carnitine synthesis / carnitine biosynthetic process / iron ion binding / mitochondrion / extracellular exosome / zinc ion binding / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Tars, K. / Leitans, J. / Kazaks, A. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2014 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4bgm.cif.gz | 100.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4bgm.ent.gz | 75 KB | Display | PDB format |
PDBx/mmJSON format | 4bgm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4bgm_validation.pdf.gz | 454.6 KB | Display | wwPDB validaton report |
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Full document | 4bgm_full_validation.pdf.gz | 455.5 KB | Display | |
Data in XML | 4bgm_validation.xml.gz | 18.1 KB | Display | |
Data in CIF | 4bgm_validation.cif.gz | 26.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bg/4bgm ftp://data.pdbj.org/pub/pdb/validation_reports/bg/4bgm | HTTPS FTP |
-Related structure data
Related structure data | 4bg1C 4bgkC 4bhfC 4bhiC 4c5wC 3o2gS C: citing same article (ref.) S: Starting model for refinement |
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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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-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.) HOMO SAPIENS (human) / Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast) / Strain (production host): AH22 References: UniProt: O75936, gamma-butyrobetaine dioxygenase |
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-Non-polymers , 5 types, 272 molecules
#2: Chemical | ChemComp-OGA / | ||||
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#3: Chemical | ChemComp-DLT / | ||||
#4: Chemical | #5: Chemical | ChemComp-16D / | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: 20 % PEG 3350, 1.5 % 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: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1.03911 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Mar 31, 2011 / Details: MIRRORS |
Radiation | Monochromator: DOUBLE SI CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03911 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→45.27 Å / Num. obs: 17821 / % possible obs: 99.2 % / Redundancy: 3.3 % / Biso Wilson estimate: 36.529 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 2.4→2.53 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 2.6 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3O2G Resolution: 2.4→45.27 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.909 / SU B: 7.338 / SU ML: 0.17 / Cross valid method: THROUGHOUT / ESU R: 0.399 / ESU R Free: 0.252 / 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: 27.691 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→45.27 Å
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Refine LS restraints |
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