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- PDB-6edh: Taurine:2OG dioxygenase (TauD) bound to the vanadyl ion, taurine,... -

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Basic information

Entry
Database: PDB / ID: 6edh
TitleTaurine:2OG dioxygenase (TauD) bound to the vanadyl ion, taurine, and succinate
ComponentsAlpha-ketoglutarate-dependent taurine dioxygenase
KeywordsOXIDOREDUCTASE / hydroxylase / 2-oxo-glutarate / vanadyl ion
Function / homology
Function and homology information


taurine catabolic process / taurine dioxygenase complex / taurine dioxygenase / taurine dioxygenase activity / sulfur compound metabolic process / L-ascorbic acid binding / ferrous iron binding / protein homotetramerization / identical protein binding / cytoplasm
Similarity search - Function
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 / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / DI(HYDROXYETHYL)ETHER / SUCCINIC ACID / 2-AMINOETHANESULFONIC ACID / oxovanadium(2+) / Alpha-ketoglutarate-dependent taurine dioxygenase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73000401657 Å
AuthorsDavis, K.M. / Altmyer, M. / Boal, A.K.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM119707 United States
Arnold and Mabel Beckman Foundation United States
CitationJournal: Biochemistry / Year: 2019
Title: Structure of a Ferryl Mimic in the Archetypal Iron(II)- and 2-(Oxo)-glutarate-Dependent Dioxygenase, TauD.
Authors: Davis, K.M. / Altmyer, M. / Martinie, R.J. / Schaperdoth, I. / Krebs, C. / Bollinger Jr., J.M. / Boal, A.K.
History
DepositionAug 9, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2019Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 23, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 13, 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
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_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_asym_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
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alpha-ketoglutarate-dependent taurine dioxygenase
B: Alpha-ketoglutarate-dependent taurine dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,88210
Polymers64,9072
Non-polymers9758
Water5,423301
1
A: Alpha-ketoglutarate-dependent taurine dioxygenase
hetero molecules

A: Alpha-ketoglutarate-dependent taurine dioxygenase
hetero molecules

B: Alpha-ketoglutarate-dependent taurine dioxygenase
hetero molecules

B: Alpha-ketoglutarate-dependent taurine dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,76320
Polymers129,8144
Non-polymers1,95016
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_444-x-1/2,y-1/2,-z-11
crystal symmetry operation4_554x+1/2,-y+1/2,-z-11
Buried area9140 Å2
ΔGint-7 kcal/mol
Surface area46480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.410, 54.199, 87.385
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
Components on special symmetry positions
IDModelComponents
11A-488-

HOH

21B-406-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Alpha-ketoglutarate-dependent taurine dioxygenase / 2-aminoethanesulfonate dioxygenase / Sulfate starvation-induced protein 3 / SSI3


Mass: 32453.467 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: tauD, ssiD, yaiG, b0368, JW0360 / Production host: Escherichia coli (E. coli) / References: UniProt: P37610, taurine dioxygenase

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Non-polymers , 8 types, 309 molecules

#2: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-VVO / oxovanadium(2+)


Mass: 66.941 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: OV
#4: Chemical ChemComp-SIN / SUCCINIC ACID / Succinic acid


Mass: 118.088 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O4
#5: Chemical ChemComp-TAU / 2-AMINOETHANESULFONIC ACID / Taurine


Mass: 125.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H7NO3S
#6: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#8: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 301 / 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: 2.15 Å3/Da / Density % sol: 42.79 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Na acetate, pH 4.25, and 24% (w/v) PEG 300

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.73→36.53 Å / Num. obs: 58939 / % possible obs: 99 % / Redundancy: 13.1 % / Biso Wilson estimate: 27.4529191957 Å2 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.019 / Net I/σ(I): 23.27
Reflection shellResolution: 1.73→1.79 Å / Redundancy: 13.3 % / Mean I/σ(I) obs: 1.96 / Num. unique obs: 5830 / Rpim(I) all: 0.325 / % possible all: 99.25

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-2000data scaling
BALBESphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GY9A

Resolution: 1.73000401657→36.3536405369 Å / SU ML: 0.17106013969 / Cross valid method: FREE R-VALUE / σ(F): 1.3364822269 / Phase error: 20.8119327506
RfactorNum. reflection% reflection
Rfree0.204767620386 1712 2.90607866103 %
Rwork0.182788808811 --
obs0.183402761187 58911 98.9668380204 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 32.4592989629 Å2
Refinement stepCycle: LAST / Resolution: 1.73000401657→36.3536405369 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4541 0 6 301 4848
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005057452104074729
X-RAY DIFFRACTIONf_angle_d0.7391420577996444
X-RAY DIFFRACTIONf_chiral_restr0.0512155479686687
X-RAY DIFFRACTIONf_plane_restr0.00445052146303850
X-RAY DIFFRACTIONf_dihedral_angle_d18.779264731717
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.73-1.78090.2859377528891410.2326688307064717X-RAY DIFFRACTION99.2035940372
1.7809-1.83840.2539155084261410.2164065509314698X-RAY DIFFRACTION99.3226600985
1.8384-1.90410.2237342886911410.205532731644740X-RAY DIFFRACTION99.1670052824
1.9041-1.98030.2473671512071410.1920816558984680X-RAY DIFFRACTION98.8112318098
1.9803-2.07040.2452655059261410.1829213975644724X-RAY DIFFRACTION98.982706002
2.0704-2.17960.211519763021420.178964088954741X-RAY DIFFRACTION98.8661672403
2.1796-2.31610.2187011083891420.1810313220164719X-RAY DIFFRACTION99.1029561672
2.3161-2.49490.2175646090071410.1838334651084745X-RAY DIFFRACTION98.6472844741
2.4949-2.74590.210838440061420.1833760019414753X-RAY DIFFRACTION98.6298609712
2.7459-3.14310.2218901815441430.1876436538154767X-RAY DIFFRACTION98.5350190648
3.1431-3.95920.1758139290571470.1797836118334875X-RAY DIFFRACTION99.5243757432
3.9592-36.36170.1847609562341500.1739888382015040X-RAY DIFFRACTION98.8194973343

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