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- PDB-3o2g: Crystal Structure of Human gamma-butyrobetaine,2-oxoglutarate dio... -

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Basic information

Entry
Database: PDB / ID: 3o2g
TitleCrystal Structure of Human gamma-butyrobetaine,2-oxoglutarate dioxygenase 1 (BBOX1)
ComponentsGamma-butyrobetaine dioxygenase
KeywordsOXIDOREDUCTASE / GAMMA-BUTYROBETAINE HYDROXYLASE / GAMMA-BUTYROBETAINE / 2-OXOGLUTARATE DIOXYGENASE 1 / Structural Genomics / Structural Genomics Consortium / SGC
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
3-CARBOXY-N,N,N-TRIMETHYLPROPAN-1-AMINIUM / N-OXALYLGLYCINE / Gamma-butyrobetaine dioxygenase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.78 Å
AuthorsKrojer, T. / Kochan, G. / McDonough, M.A. / von Delft, F. / Leung, I.K.H. / Henry, L. / Claridge, T.D.W. / Pilka, E. / Ugochukwu, E. / Muniz, J. ...Krojer, T. / Kochan, G. / McDonough, M.A. / von Delft, F. / Leung, I.K.H. / Henry, L. / Claridge, T.D.W. / Pilka, E. / Ugochukwu, E. / Muniz, J. / Filippakopoulos, P. / Bountra, C. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / Kavanagh, K.L. / Schofield, C.J. / Oppermann, U. / Structural Genomics Consortium (SGC)
CitationJournal: Chem. Biol. / Year: 2010
Title: Structural and mechanistic studies on gamma-butyrobetaine hydroxylase.
Authors: Leung, I.K. / Krojer, T.J. / Kochan, G.T. / Henry, L. / von Delft, F. / Claridge, T.D. / Oppermann, U. / McDonough, M.A. / Schofield, C.J.
History
DepositionJul 22, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 20, 2019Group: Data collection / Database references / Derived calculations
Category: citation / citation_author / pdbx_struct_special_symmetry
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_ref_seq_dif.details / _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)45,59610
Polymers44,8621
Non-polymers7349
Water7,873437
1
A: Gamma-butyrobetaine dioxygenase
hetero molecules

A: Gamma-butyrobetaine dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,19320
Polymers89,7242
Non-polymers1,46918
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area10590 Å2
ΔGint-97 kcal/mol
Surface area30480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.386, 107.386, 204.919
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-659-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Gamma-butyrobetaine dioxygenase / Gamma-butyrobetaine / 2-oxoglutarate dioxygenase / Gamma-butyrobetaine hydroxylase / Gamma-BBH


Mass: 44861.945 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BBOX1, BBH, BBOX / Plasmid: PFBOH-LIC-BSE / Production host: TRICHOPLUSIA NI (cabbage looper) / Strain (production host): DH10BAC
References: UniProt: O75936, gamma-butyrobetaine dioxygenase

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Non-polymers , 5 types, 446 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-OGA / N-OXALYLGLYCINE


Mass: 147.086 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H5NO5 / Comment: inhibitor*YM
#4: Chemical ChemComp-NM2 / 3-CARBOXY-N,N,N-TRIMETHYLPROPAN-1-AMINIUM


Mass: 146.207 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H16NO2
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 437 / 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: 2.53 Å3/Da / Density % sol: 51.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2M AMMONIUM CITRATE, 20% PEG 3350, 6% DIAMINE HEXAN, 10MM ZNSO4, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 7, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.78→84.69 Å / Num. all: 43809 / Num. obs: 43809 / % possible obs: 100 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 11 % / Biso Wilson estimate: 18.6 Å2 / Rmerge(I) obs: 0.14 / Rsym value: 0.14 / Net I/σ(I): 12.3

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Processing

Software
NameVersionClassification
GDAdata collection
SHELXDphasing
REFMAC5.6.0066refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MIR / Resolution: 1.78→28.98 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.955 / SU B: 3.583 / SU ML: 0.062 / Cross valid method: THROUGHOUT / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.17633 2226 5.1 %RANDOM
Rwork0.14717 ---
all0.14869 43809 --
obs0.14869 41560 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.971 Å2
Baniso -1Baniso -2Baniso -3
1-0.29 Å20.15 Å20 Å2
2--0.29 Å20 Å2
3----0.44 Å2
Refinement stepCycle: LAST / Resolution: 1.78→28.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3109 0 42 437 3588
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0223321
X-RAY DIFFRACTIONr_bond_other_d0.0010.022260
X-RAY DIFFRACTIONr_angle_refined_deg1.5541.954519
X-RAY DIFFRACTIONr_angle_other_deg0.92635507
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3565418
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.98224.074162
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.36615566
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.711519
X-RAY DIFFRACTIONr_chiral_restr0.0980.2491
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213714
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02704
LS refinement shellResolution: 1.78→1.826 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 179 -
Rwork0.267 3018 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.88460.0805-0.85190.65380.37842.08470.00190.08660.0335-0.0321-0.06280.2041-0.1005-0.26270.06090.03190.02350.00650.0412-0.01120.0771-10.439729.8216123.8685
20.7789-0.2867-0.04811.05380.08070.7927-0.04440.04960.0052-0.02720.02130.085-0.1232-0.05650.02310.02690.0152-0.00680.04770.00350.008412.425630.212787.7316
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 108
2X-RAY DIFFRACTION2A109 - 384

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