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

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Basic information

Entry
Database: PDB / ID: 4bgk
TitleThree dimensional structure of human gamma-butyrobetaine hydroxylase in complex with (3-(Trimethylammonio)propyl)phosphinate
ComponentsGAMMA-BUTYROBETAINE DIOXYGENASE
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


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
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 ...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 / N-OXALYLGLYCINE / trimethyl(3-oxidanylphosphonoylpropyl)azanium / Gamma-butyrobetaine dioxygenase
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.18 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 27, 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 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Experimental preparation / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / exptl_crystal_grow / 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 / _exptl_crystal_grow.temp / _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_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_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.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)45,3356
Polymers44,7751
Non-polymers5605
Water6,630368
1
A: GAMMA-BUTYROBETAINE DIOXYGENASE
hetero molecules

A: GAMMA-BUTYROBETAINE DIOXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,67012
Polymers89,5502
Non-polymers1,12110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area9580 Å2
ΔGint-112.7 kcal/mol
Surface area30900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.720, 107.720, 204.710
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-2351-

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, 373 molecules

#2: Chemical ChemComp-OGA / N-OXALYLGLYCINE


Mass: 147.086 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H5NO5 / Comment: inhibitor*YM
#3: Chemical ChemComp-RTK / trimethyl(3-oxidanylphosphonoylpropyl)azanium


Mass: 166.178 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H17NO2P
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / 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.: 368 / 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: 1.01
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 5, 2011 / Details: MIRRORS
RadiationMonochromator: DOUBLE SI CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.01 Å / Relative weight: 1
ReflectionResolution: 2.18→37.55 Å / Num. obs: 23613 / % possible obs: 97.9 % / Redundancy: 2.5 % / Biso Wilson estimate: 21.614 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 6.2
Reflection shellResolution: 2.18→2.3 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 2.2 / % possible all: 99.5

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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: 2.18→42.44 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.934 / SU B: 4.173 / SU ML: 0.107 / Cross valid method: THROUGHOUT / ESU R: 0.21 / ESU R Free: 0.171 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.19365 1216 5.1 %RANDOM
Rwork0.14554 ---
obs0.148 22547 98.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.266 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20.1 Å20 Å2
2--0.1 Å20 Å2
3----0.31 Å2
Refinement stepCycle: LAST / Resolution: 2.18→42.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3116 0 30 368 3514
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0193237
X-RAY DIFFRACTIONr_bond_other_d0.0010.023041
X-RAY DIFFRACTIONr_angle_refined_deg1.3441.9474385
X-RAY DIFFRACTIONr_angle_other_deg0.72136993
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3815390
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.78323.924158
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.69815549
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6191519
X-RAY DIFFRACTIONr_chiral_restr0.0770.2471
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023653
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02783
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: 2.182→2.239 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.258 76 -
Rwork0.189 1621 -
obs--97.36 %

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