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- PDB-4c8r: Human gamma-butyrobetaine dioxygenase (BBOX1) in complex with Ni(... -

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Basic information

Entry
Database: PDB / ID: 4c8r
TitleHuman gamma-butyrobetaine dioxygenase (BBOX1) in complex with Ni(II) and N-(3-hydroxypicolinoyl)-S-(pyridin-2-ylmethyl)-L-cysteine (AR692B)
ComponentsGAMMA-BUTYROBETAINE DIOXYGENASE
KeywordsOXIDOREDUCTASE / NON-HEME / IRON / 2-OXOGLUTARATE / DIOXYGENASE 1 / DSBH / FACIAL TRIAD / GAMMA-BUTYROBETAINE / HYDROXYLASE
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
Chem-6YT / NICKEL (II) ION / Gamma-butyrobetaine dioxygenase
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.82 Å
AuthorsChowdhury, R. / Rydzik, A.M. / Kochan, G.T. / McDonough, M.A. / Schofield, C.J.
CitationJournal: Chem Sci / Year: 2014
Title: Modulating carnitine levels by targeting its biosynthesis pathway - selective inhibition of gamma-butyrobetaine hydroxylase.
Authors: Rydzik, A.M. / Chowdhury, R. / Kochan, G.T. / Williams, S.T. / McDonough, M.A. / Kawamura, A. / Schofield, C.J.
History
DepositionOct 1, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 14, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jan 30, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.3Feb 6, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Dec 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_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_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
B: GAMMA-BUTYROBETAINE DIOXYGENASE
C: GAMMA-BUTYROBETAINE DIOXYGENASE
D: GAMMA-BUTYROBETAINE DIOXYGENASE
E: GAMMA-BUTYROBETAINE DIOXYGENASE
F: GAMMA-BUTYROBETAINE DIOXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)272,78538
Polymers269,1726
Non-polymers3,61432
Water8,431468
1
A: GAMMA-BUTYROBETAINE DIOXYGENASE
B: GAMMA-BUTYROBETAINE DIOXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,94913
Polymers89,7242
Non-polymers1,22511
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8620 Å2
ΔGint-45.6 kcal/mol
Surface area33190 Å2
MethodPISA
2
C: GAMMA-BUTYROBETAINE DIOXYGENASE
D: GAMMA-BUTYROBETAINE DIOXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,88712
Polymers89,7242
Non-polymers1,16310
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8250 Å2
ΔGint-25.5 kcal/mol
Surface area33660 Å2
MethodPISA
3
E: GAMMA-BUTYROBETAINE DIOXYGENASE
F: GAMMA-BUTYROBETAINE DIOXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,94913
Polymers89,7242
Non-polymers1,22511
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8020 Å2
ΔGint-22.7 kcal/mol
Surface area32880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)195.744, 91.659, 167.132
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 6 molecules ABCDEF

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


Mass: 44861.945 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / 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, 500 molecules

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


Mass: 58.693 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ni
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-6YT / N-(3-hydroxypicolinoyl)-S-(pyridin-2-ylmethyl)-L-cysteine


Mass: 333.362 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C15H15N3O4S
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 468 / 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: 2.82 Å3/Da / Density % sol: 56.36 % / Description: NONE
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2 M AMMONIUM CITRATE, 10MM NISO4, 2% 1,6-DIAMINOHEXANE, 19% PEG 3350, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 14, 2013 / Details: MIRRORS
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.82→48.42 Å / Num. obs: 71043 / % possible obs: 97.8 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Biso Wilson estimate: 58.9 Å2 / Rmerge(I) obs: 0.2 / Net I/σ(I): 4.01
Reflection shellResolution: 2.82→2.9 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 1.91 / % possible all: 99.3

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Processing

Software
NameVersionClassification
CNS1.3refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3O2G

3o2g


Resolution: 2.82→48.42 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 66066.14 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.244 3580 5 %RANDOM
Rwork0.215 ---
obs0.215 71043 97.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 37.1039 Å2 / ksol: 0.32 e/Å3
Displacement parametersBiso mean: 63.1 Å2
Baniso -1Baniso -2Baniso -3
1--0.39 Å20 Å20 Å2
2---9.93 Å20 Å2
3---10.32 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.54 Å0.44 Å
Refinement stepCycle: LAST / Resolution: 2.82→48.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18678 0 206 468 19352
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.82
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 2.82→2.9 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.362 342 4.8 %
Rwork0.313 7115 -
obs--99.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4692.PAR692.TOP
X-RAY DIFFRACTION5EDO.PAREDO.TOP

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