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- PDB-3swt: Crystal Structure of the Taurine catabolism dioxygenase, TauD fro... -

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Basic information

Entry
Database: PDB / ID: 3swt
TitleCrystal Structure of the Taurine catabolism dioxygenase, TauD from Mycobacterium marinum
ComponentsTaurine catabolism dioxygenase, TauD
KeywordsOXIDOREDUCTASE / Taurine catabolism dioxygenase / TauD / Seattle Structural Genomics Center for Infectious Disease / SSGCID / dioxygenase
Function / homology
Function and homology information


dioxygenase activity / metal ion binding
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
: / DI(HYDROXYETHYL)ETHER / Taurine catabolism dioxygenase, TauD
Similarity search - Component
Biological speciesMycobacterium marinum M (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.05 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Tuberculosis (Edinb) / Year: 2015
Title: Increasing the structural coverage of tuberculosis drug targets.
Authors: Baugh, L. / Phan, I. / Begley, D.W. / Clifton, M.C. / Armour, B. / Dranow, D.M. / Taylor, B.M. / Muruthi, M.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Dieterich, S.H. / Staker, B.L. / ...Authors: Baugh, L. / Phan, I. / Begley, D.W. / Clifton, M.C. / Armour, B. / Dranow, D.M. / Taylor, B.M. / Muruthi, M.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Dieterich, S.H. / Staker, B.L. / Gardberg, A.S. / Choi, R. / Hewitt, S.N. / Napuli, A.J. / Myers, J. / Barrett, L.K. / Zhang, Y. / Ferrell, M. / Mundt, E. / Thompkins, K. / Tran, N. / Lyons-Abbott, S. / Abramov, A. / Sekar, A. / Serbzhinskiy, D. / Lorimer, D. / Buchko, G.W. / Stacy, R. / Stewart, L.J. / Edwards, T.E. / Van Voorhis, W.C. / Myler, P.J.
History
DepositionJul 14, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 12, 2014Group: Structure summary
Revision 1.2Mar 11, 2015Group: Database references
Revision 1.3Apr 15, 2015Group: Database references
Revision 1.4Nov 8, 2017Group: Refinement description / Category: software
Revision 1.5Feb 28, 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 / pdbx_struct_special_symmetry / 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.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: Taurine catabolism dioxygenase, TauD
B: Taurine catabolism dioxygenase, TauD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,7866
Polymers66,5062
Non-polymers2804
Water5,819323
1
A: Taurine catabolism dioxygenase, TauD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3713
Polymers33,2531
Non-polymers1182
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Taurine catabolism dioxygenase, TauD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4153
Polymers33,2531
Non-polymers1622
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Taurine catabolism dioxygenase, TauD
hetero molecules

A: Taurine catabolism dioxygenase, TauD
hetero molecules

B: Taurine catabolism dioxygenase, TauD
hetero molecules

B: Taurine catabolism dioxygenase, TauD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,57212
Polymers133,0134
Non-polymers5608
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_756-x+2,y,-z+11
crystal symmetry operation3_566x+1/2,-y+1,-z+3/21
crystal symmetry operation4_664-x+3/2,-y+1,z-1/21
Buried area6380 Å2
ΔGint-24 kcal/mol
Surface area38300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.098, 89.078, 104.703
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221
Components on special symmetry positions
IDModelComponents
11A-419-

HOH

21A-436-

HOH

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Components

#1: Protein Taurine catabolism dioxygenase, TauD


Mass: 33253.176 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium marinum M (bacteria) / Strain: ATCC BAA-535 / M / Gene: tauD, MMAR_1141 / Production host: Escherichia coli (E. coli) / References: UniProt: B2HD26
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 323 / 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: 2.42 Å3/Da / Density % sol: 49.23 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 44 mg/ml. 20% PEG 3350, 200mM potassium citrate. 25% ethylene glycol (cryoprotection), pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 24, 2011
RadiationMonochromator: Asymmetric curved crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 40618 / % possible obs: 98.5 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.104 / Χ2: 0.997 / Net I/σ(I): 7.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.05-2.094.80.45718370.924190.5
2.09-2.125.10.43218690.925192.9
2.12-2.165.20.42319190.932194.1
2.16-2.215.40.40419130.966195.7
2.21-2.265.50.35420061.054198.8
2.26-2.315.80.3820181.005199.4
2.31-2.3760.34520590.983199.8
2.37-2.436.10.3120060.9961100
2.43-2.56.20.25720690.9991100
2.5-2.586.10.22220251.051100
2.58-2.686.20.19920541.0681100
2.68-2.786.20.16420561.0771100
2.78-2.916.10.12920521.0161100
2.91-3.066.10.10920531.0061100
3.06-3.256.10.08720610.9281100
3.25-3.5160.08120760.922199.9
3.51-3.8660.07320751.0761100
3.86-4.425.90.0621061.071199.9
4.42-5.565.80.04221230.936199.9
5.56-505.80.03322410.938199.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 52.02 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å37.79 Å
Translation2.5 Å37.79 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→50 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.926 / WRfactor Rfree: 0.2167 / WRfactor Rwork: 0.1751 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8608 / SU B: 8.649 / SU ML: 0.106 / SU R Cruickshank DPI: 0.1709 / SU Rfree: 0.1566 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2263 2029 5 %RANDOM
Rwork0.1859 ---
obs0.1879 40461 98.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 60.13 Å2 / Biso mean: 25.4653 Å2 / Biso min: 7.7 Å2
Baniso -1Baniso -2Baniso -3
1-2.23 Å20 Å20 Å2
2---1.78 Å20 Å2
3----0.44 Å2
Refinement stepCycle: LAST / Resolution: 2.05→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3798 0 13 323 4134
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0213937
X-RAY DIFFRACTIONr_bond_other_d0.0020.022574
X-RAY DIFFRACTIONr_angle_refined_deg1.3571.935378
X-RAY DIFFRACTIONr_angle_other_deg0.936238
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4525498
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.55623.469196
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.56815590
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7421535
X-RAY DIFFRACTIONr_chiral_restr0.0810.2611
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214472
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02827
X-RAY DIFFRACTIONr_mcbond_it0.6991.52454
X-RAY DIFFRACTIONr_mcbond_other0.1741.5996
X-RAY DIFFRACTIONr_mcangle_it1.30723935
X-RAY DIFFRACTIONr_scbond_it2.07831483
X-RAY DIFFRACTIONr_scangle_it3.2944.51436
LS refinement shellResolution: 2.051→2.104 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 133 -
Rwork0.229 2556 -
all-2689 -
obs--90.6 %
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)
10.42460.013-0.08641.296-0.06910.8329-0.04970.0218-0.0020.0851-0.00560.14060.0239-0.07250.05530.0332-0.01790.02780.0283-0.01660.033356.630328.775362.051
20.4952-0.0999-0.15971.0277-0.16770.8974-0.07170.001-0.0152-0.0955-0.0262-0.06840.09120.03620.0980.0720.01550.0490.02360.0120.038643.798217.627291.619
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 296
2X-RAY DIFFRACTION1A299 - 300
3X-RAY DIFFRACTION1A301 - 456
4X-RAY DIFFRACTION2B4 - 297
5X-RAY DIFFRACTION2B299 - 300
6X-RAY DIFFRACTION2B301 - 467

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