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- PDB-3ms5: Crystal Structure of Human gamma-butyrobetaine,2-oxoglutarate dio... -

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Basic information

Entry
Database: PDB / ID: 3ms5
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
NICKEL (II) ION / N-OXALYLGLYCINE / 2-(2-carboxyethyl)-1,1,1-trimethyldiazanium / Gamma-butyrobetaine dioxygenase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.82 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
DepositionApr 29, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Mar 20, 2019Group: Data collection / Database references / Category: citation
Revision 1.4Feb 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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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)45,83914
Polymers44,8621
Non-polymers97713
Water7,440413
1
A: Gamma-butyrobetaine dioxygenase
hetero molecules

A: Gamma-butyrobetaine dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,67828
Polymers89,7242
Non-polymers1,95426
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area12750 Å2
ΔGint-12 kcal/mol
Surface area29930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.366, 107.366, 205.054
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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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: BBH, BBOX, BBOX1 / 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 , 6 types, 426 molecules

#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-OGA / N-OXALYLGLYCINE


Mass: 147.086 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H5NO5 / Comment: inhibitor*YM
#5: Chemical ChemComp-REE / 2-(2-carboxyethyl)-1,1,1-trimethyldiazanium


Mass: 147.195 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15N2O2 / Comment: medication*YM
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 413 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 51.48 %
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

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONDiamond I0311.0084
SYNCHROTRONDiamond I0220.9795
Detector
TypeIDDetectorDate
MARMOSAIC 225 mm CCD1CCDOct 24, 2009
MARMOSAIC 225 mm CCD2CCDFeb 4, 2010
RadiationProtocol: SIRAS / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.00841
20.97951
ReflectionResolution: 1.82→84.69 Å / Num. obs: 40755 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Rmerge(I) obs: 0.083 / Rsym value: 0.083 / Net I/σ(I): 12.3
Reflection shellResolution: 1.82→1.92 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.452 / Mean I/σ(I) obs: 3.3 / Num. unique all: 30263 / Rsym value: 0.452 / % possible all: 96.2

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Processing

Software
NameVersionClassification
MAR345data collection
SHARPphasing
REFMAC5.6.0066refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SIRAS / Resolution: 1.82→19.45 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.955 / SU B: 4.114 / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.18257 2059 5.1 %RANDOM
Rwork0.14671 ---
all0.14856 38693 --
obs0.14856 38693 99.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.778 Å2
Baniso -1Baniso -2Baniso -3
1-1.11 Å20.56 Å20 Å2
2--1.11 Å20 Å2
3----1.67 Å2
Refinement stepCycle: LAST / Resolution: 1.82→19.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3101 0 58 413 3572
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0223286
X-RAY DIFFRACTIONr_bond_other_d0.0010.022246
X-RAY DIFFRACTIONr_angle_refined_deg1.61.9514450
X-RAY DIFFRACTIONr_angle_other_deg0.9623.0015450
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2665403
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.12324.088159
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.7615552
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5271518
X-RAY DIFFRACTIONr_chiral_restr0.1040.2481
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023645
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02692
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_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.82→1.867 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 130 -
Rwork0.236 2617 -
obs--91.9 %
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)
12.4516-0.0821-0.85710.60780.26061.844-0.0080.1481-0.0309-0.017-0.08620.2262-0.1191-0.25780.09420.03720.02060.01080.0538-0.03520.0979-10.556429.7572123.9404
20.8156-0.2558-0.1091.17240.16880.9614-0.08430-0.04980.00150.01930.1292-0.123-0.07130.06490.03530.0278-0.00590.0489-0.00680.017612.369530.200487.7978
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 108
2X-RAY DIFFRACTION2A109 - 384

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