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- PDB-1gy9: Taurine/alpha-ketoglutarate Dioxygenase from Escherichia coli -

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Basic information

Entry
Database: PDB / ID: 1gy9
TitleTaurine/alpha-ketoglutarate Dioxygenase from Escherichia coli
ComponentsALPHA-KETOGLUTARATE-DEPENDENT TAURINE DIOXYGENASE
KeywordsOXIDOREDUCTASE / TAURINE / SULPHUR METABOLISM / OXYGENASE / ALPHA-KETOGLUTARATE / TAUD / TFDA
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsElkins, J.M. / Burzlaff, N.I. / Ryle, M.J. / Lloyd, J.S. / Clifton, I.J. / 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.C. / Lloyd, J.S. / Burzlaff, N.I. / Baldwin, J.E. / Hausinger, R.P. / Roach, P.L.
History
DepositionApr 22, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 26, 2002Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 13, 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.ptnr1_symmetry / _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.ptnr3_symmetry / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _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)65,6179
Polymers64,9072
Non-polymers7107
Water39622
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
Water724
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 area9380 Å2
ΔGint-83.43 kcal/mol
Surface area43450 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)131,34620
Polymers129,8144
Non-polymers1,53216
Water724
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 area9300 Å2
ΔGint-75.59 kcal/mol
Surface area43880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.786, 116.786, 201.937
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A3 - 351
2111B3 - 351

NCS oper: (Code: given
Matrix: (-0.85598, 0.51686, -0.01248), (-0.51699, -0.85591, 0.0118), (-0.00458, 0.01655, 0.99985)
Vector: 57.74625, 57.79279, 33.19389)

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Components

#1: Protein ALPHA-KETOGLUTARATE-DEPENDENT TAURINE DIOXYGENASE


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-FE / FE (III) ION


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


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


Mass: 146.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H6O5
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / Source method: isolated from a natural source / Formula: H2O
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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.935
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 15, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.935 Å / Relative weight: 1
ReflectionResolution: 2.5→90 Å / Num. obs: 28679 / % possible obs: 99.3 % / Redundancy: 8 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 7.4
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.311 / Mean I/σ(I) obs: 2.3 / % possible all: 99.1

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Processing

Software
NameVersionClassification
REFMAC5refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GQW

1gqw


Resolution: 2.5→45.18 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.894 / SU B: 12.51 / SU ML: 0.286 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.501 / ESU R Free: 0.315 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS RESIDUES WITH DISORDERED SIDE-CHAINS WERE MODELED AS ALANINE
RfactorNum. reflection% reflectionSelection details
Rfree0.293 2840 9.9 %RANDOM
Rwork0.261 ---
obs0.264 25742 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Refinement stepCycle: LAST / Resolution: 2.5→45.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4357 0 37 22 4416
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0214529
X-RAY DIFFRACTIONr_bond_other_d0.0020.024011
X-RAY DIFFRACTIONr_angle_refined_deg
X-RAY DIFFRACTIONr_angle_other_deg2.0451.9286186
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg1.02139291
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1320.2676
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025093
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02942
X-RAY DIFFRACTIONr_nbd_refined0.2460.31099
X-RAY DIFFRACTIONr_nbd_other0.2350.34282
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.1070.52
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.5272
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.107
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3720.318
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2970.361
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.260.59
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6871.52783
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.21824485
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.13231746
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.4494.51701
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 4025 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Atight positional0.060.05
2Btight positional0.060.05
1Atight thermal0.170.5
2Btight thermal0.170.5
LS refinement shellResolution: 2.5→2.56 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.358 219
Rwork0.289 1837
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)
12.3505-1.61530.82953.0273-0.38695.24090.3820.1056-0.4895-0.6365-0.480.5431.1537-0.12690.0980.59060.3323-0.01840.1986-0.06190.22929.10534.33546.365
22.2538-0.0214-0.25862.8065-0.12057.00460.65170.32570.5302-0.4687-0.18110.1818-0.939-0.391-0.47071.39860.49860.16330.2730.12960.446149.68813.43779.664
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 282
2X-RAY DIFFRACTION2B3 - 282

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