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- PDB-1gqw: Taurine/alpha-ketoglutarate Dioxygenase from Escherichia coli -

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Basic information

Entry
Database: PDB / ID: 1gqw
TitleTaurine/alpha-ketoglutarate Dioxygenase from Escherichia coli
ComponentsALPHA-KETOGLUTARATE-DEPENDENT TAURINE DIOXYGENASE
KeywordsOXIDOREDUCTASE / TAURINE / SULPHUR METABOLISM / OXYGENASE / ALPHA-KETOGLUTARATE / TAUD / TFDA / DIOXYGENASE
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
2-OXOGLUTARIC ACID / : / 2-AMINOETHANESULFONIC ACID / Alpha-ketoglutarate-dependent taurine dioxygenase
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / MIR / Resolution: 3 Å
AuthorsElkins, J.M. / Ryle, M.J. / Clifton, I.J. / Dunning-Hotopp, J.C. / Lloyd, J.S. / Burzlaff, N.I. / Baldwin, J.E. / Hausinger, R.P. / Roach, P.L.
CitationJournal: Biochemistry / Year: 2002
Title: X-Ray Crystal Structure of Escherichia Coli Taurine/Alpha-Ketoglutarate Dioxygenase Complexed to Ferrous Iron and Substrates
Authors: Elkins, J.M. / Ryle, M.J. / Clifton, I.J. / Dunning Hotopp, J. / Lloyd, J.S. / Burzlaff, N.I. / Baldwin, J.E. / Hausinger, R.P. / Roach, P.L.
History
DepositionDec 5, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 18, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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.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: ALPHA-KETOGLUTARATE-DEPENDENT TAURINE DIOXYGENASE
B: ALPHA-KETOGLUTARATE-DEPENDENT TAURINE DIOXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,5618
Polymers64,9072
Non-polymers6546
Water0
1
B: ALPHA-KETOGLUTARATE-DEPENDENT TAURINE DIOXYGENASE
hetero molecules

B: 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)131,12216
Polymers129,8144
Non-polymers1,30812
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_655-x+1,-y,z1
crystal symmetry operation8_556x-y,-y,-z+11
crystal symmetry operation11_656-x+y+1,y,-z+11
Buried area9200 Å2
ΔGint-71.94 kcal/mol
Surface area43130 Å2
MethodPISA
2
A: ALPHA-KETOGLUTARATE-DEPENDENT TAURINE DIOXYGENASE
hetero molecules

A: ALPHA-KETOGLUTARATE-DEPENDENT TAURINE DIOXYGENASE
hetero molecules

A: ALPHA-KETOGLUTARATE-DEPENDENT TAURINE DIOXYGENASE
hetero molecules

A: ALPHA-KETOGLUTARATE-DEPENDENT TAURINE DIOXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,12216
Polymers129,8144
Non-polymers1,30812
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-x+1,-y+1,z1
crystal symmetry operation7_555y,x,-z+2/31
crystal symmetry operation10_665-y+1,-x+1,-z+2/31
Buried area9250 Å2
ΔGint-73.5 kcal/mol
Surface area43890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.850, 116.850, 201.910
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.85901, 0.51171, -0.01591), (-0.51188, -0.859, 0.00965), (-0.00873, 0.01643, 0.99983)
Vector: 58.22111, 57.95159, 33.43064)

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Components

#1: Protein ALPHA-KETOGLUTARATE-DEPENDENT TAURINE DIOXYGENASE / TAURINE DIOXYGENASE / 2-AMINOETHANESULFONATE DIOXYGENASE / SULFATE STARVATION-INDUCED PROTEIN 3


Mass: 32453.467 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P37610, taurine dioxygenase
#2: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-TAU / 2-AMINOETHANESULFONIC ACID / Taurine


Mass: 125.147 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H7NO3S
#4: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID / Α-Ketoglutaric acid


Mass: 146.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H6O5
Compound detailsCONVERTS ALPHA KETOGLUTARATE AND TAURINE INTO SULPHITE, SUCCINATE AND AMINOACETALDEHYDE.

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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: 3 Å3/Da / Density % sol: 60 %
Crystal growpH: 7.5
Details: 20-28% PEG1000, 20% ETHYLENE GLYCOL, 75MM IMIDAZOLE PH7.5, PROTEIN SOLUTION LOADED WITH FE(II), ALPHA-KETOGLUTARATE, TAURINE, DITHIOTHREITOL, pH 7.50
Crystal grow
*PLUS
Temperature: 17 ℃ / pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
118 mg/mlprotein1drop
220 mMTris1droppH7.0
3200 mMalphaKG1drop
4200 mMtaurine1droppH7.0
5100 mMdithiothreitol1drop
620-28 %PEG10001reservoir
775 mMimidazole1reservoirpH7.0
820 %ethylene glycol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 15, 2000 / Details: OSMIC
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3→40.49 Å / Num. obs: 16990 / % possible obs: 99.3 % / Redundancy: 5.9 % / Biso Wilson estimate: 60.4 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 10.5
Reflection shellResolution: 3→3.16 Å / Redundancy: 6 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 2.8 / % possible all: 99.8
Reflection
*PLUS
Num. obs: 16727 / Num. measured all: 98529
Reflection shell
*PLUS
% possible obs: 99.8 % / Rmerge(I) obs: 0.27

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Processing

Software
NameVersionClassification
CNS1refinement
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
RefinementMethod to determine structure: MIR / Resolution: 3→40.44 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 2733619.8 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0
Details: RESIDUES WITH DISORDERED SIDE-CHAINS WERE MODELED AS ALANINE
RfactorNum. reflection% reflectionSelection details
Rfree0.32 1647 9.8 %RANDOM
Rwork0.281 ---
obs0.281 16749 98.5 %-
Solvent computationSolvent model: FLAT MODEL / ksol: 0.318286 e/Å3
Displacement parametersBiso mean: 63.2 Å2
Baniso -1Baniso -2Baniso -3
1-11.22 Å22.77 Å20 Å2
2--11.22 Å20 Å2
3----22.44 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.6 Å0.48 Å
Luzzati d res low-5 Å
Luzzati sigma a0.67 Å0.52 Å
Refinement stepCycle: LAST / Resolution: 3→40.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4348 0 36 0 4384
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_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.89
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 NCSRms dev position: 0.03 Å / Weight position: 300
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.421 271 9.9 %
Rwork0.354 2464 -
obs--99.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3TAURINE_AKG_SUX_PAR.TXTTAURINE_AKG_SUX_TOP.TXT
Refinement
*PLUS
Rfactor Rfree: 0.32
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.89
LS refinement shell
*PLUS
Rfactor obs: 0.354

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