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- PDB-4bg1: Three dimensional structure of human gamma-butyrobetaine hydroxyl... -

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Basic information

Entry
Database: PDB / ID: 4bg1
TitleThree dimensional structure of human gamma-butyrobetaine hydroxylase in complex with 1-(3-Carboxypropyl)-1-methylpyrrolidin-1-ium chloride
ComponentsGAMMA-BUTYROBETAINE DIOXYGENASE
KeywordsOXIDOREDUCTASE / GAMMA-BUTYROBETAINE HYDROXYLASE / GAMMA-BBH / GAMMA-BUTYROBETAINE / 2-OXOGLUTARATE DIOXYGENASE
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
NE0471 N-terminal domain-like - #30 / Gamma-butyrobetaine hydroxylase / Gamma-butyrobetaine hydroxylase-like, N-terminal / GBBH-like, N-terminal domain superfamily / Gamma-butyrobetaine hydroxylase-like, N-terminal / NE0471 N-terminal domain-like / : / Clavaminate synthase-like / Double-stranded beta-helix / TauD/TfdA-like domain ...NE0471 N-terminal domain-like - #30 / Gamma-butyrobetaine hydroxylase / Gamma-butyrobetaine hydroxylase-like, N-terminal / GBBH-like, N-terminal domain superfamily / Gamma-butyrobetaine hydroxylase-like, N-terminal / NE0471 N-terminal domain-like / : / Clavaminate synthase-like / Double-stranded beta-helix / TauD/TfdA-like domain / Taurine catabolism dioxygenase TauD, TfdA family / Taurine dioxygenase TauD-like superfamily / 4-Layer Sandwich / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
HEXANE-1,6-DIAMINE / 1-(3-carboxypropyl)-1-methylpyrrolidin-1-ium / N-OXALYLGLYCINE / Gamma-butyrobetaine dioxygenase
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsTars, K. / Leitans, J. / Kazaks, A.
CitationJournal: 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
DepositionMar 22, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 12, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 9, 2014Group: Database references
Revision 1.2Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Jan 30, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.4Feb 6, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.5Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GAMMA-BUTYROBETAINE DIOXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4728
Polymers44,7751
Non-polymers6977
Water7,134396
1
A: GAMMA-BUTYROBETAINE DIOXYGENASE
hetero molecules

A: GAMMA-BUTYROBETAINE DIOXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,94416
Polymers89,5502
Non-polymers1,39414
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area9190 Å2
ΔGint-254.9 kcal/mol
Surface area31120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.630, 107.630, 205.530
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-2084-

HOH

21A-2378-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein GAMMA-BUTYROBETAINE DIOXYGENASE / GAMMA-BUTYROBETAINE HYDROXYLASE / GAMMA-BBH / GAMMA-BUTYROBETAINE / 2-OXOGLUTARATE DIOXYGENASE


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, 403 molecules

#2: Chemical ChemComp-OGA / N-OXALYLGLYCINE


Mass: 147.086 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H5NO5
#3: Chemical ChemComp-IVL / 1-(3-carboxypropyl)-1-methylpyrrolidin-1-ium


Mass: 172.245 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H18NO2
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-16D / HEXANE-1,6-DIAMINE / 1,6-DIAMINOHEXANE


Mass: 116.205 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H16N2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 396 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 52 % / Description: NONE
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1.04148
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 11, 2012 / Details: MULTILAYER
RadiationMonochromator: SI CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.04148 Å / Relative weight: 1
ReflectionResolution: 1.88→26.91 Å / Num. obs: 37202 / % possible obs: 97.3 % / Redundancy: 3.1 % / Biso Wilson estimate: 19.4 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 9.1
Reflection shellResolution: 1.88→1.98 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 1.9 / % possible all: 81.9

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3O2G

3o2g


Resolution: 1.89→26.92 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.948 / SU B: 2.847 / SU ML: 0.082 / Cross valid method: THROUGHOUT / ESU R: 0.126 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.19906 1833 5 %RANDOM
Rwork0.15597 ---
obs0.15808 34707 98.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.977 Å2
Baniso -1Baniso -2Baniso -3
1-0.47 Å20.47 Å20 Å2
2--0.47 Å20 Å2
3----1.53 Å2
Refinement stepCycle: LAST / Resolution: 1.89→26.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3128 0 34 396 3558
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0193261
X-RAY DIFFRACTIONr_bond_other_d0.0010.023063
X-RAY DIFFRACTIONr_angle_refined_deg1.3891.9494421
X-RAY DIFFRACTIONr_angle_other_deg0.76337051
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3335394
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.9324.049163
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.16515557
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2081520
X-RAY DIFFRACTIONr_chiral_restr0.0830.2474
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023692
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02787
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.889→1.938 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 111 -
Rwork0.277 2180 -
obs--85.29 %

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