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- PDB-3r1j: Crystal structure of Alpha-ketoglutarate-dependent taurine dioxyg... -

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Basic information

Entry
Database: PDB / ID: 3r1j
TitleCrystal structure of Alpha-ketoglutarate-dependent taurine dioxygenase from Mycobacterium avium, native form
ComponentsAlpha-ketoglutarate-dependent taurine dioxygenase
KeywordsOXIDOREDUCTASE / SSGCID / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


taurine dioxygenase / taurine 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
: / Alpha-ketoglutarate-dependent taurine dioxygenase / Alpha-ketoglutarate-dependent taurine dioxygenase
Similarity search - Component
Biological speciesMycobacterium avium (bacteria)
MethodX-RAY DIFFRACTION / 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
DepositionMar 10, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 6, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 22, 2015Group: Database references
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_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_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_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 / _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: Alpha-ketoglutarate-dependent taurine dioxygenase
B: Alpha-ketoglutarate-dependent taurine dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,77010
Polymers67,3662
Non-polymers4048
Water5,873326
1
A: Alpha-ketoglutarate-dependent taurine dioxygenase
B: Alpha-ketoglutarate-dependent taurine dioxygenase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)135,54020
Polymers134,7324
Non-polymers80916
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area9880 Å2
ΔGint-117 kcal/mol
Surface area36770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.950, 105.310, 89.250
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-300-

CL

21B-301-

CL

31A-441-

HOH

41B-302-

HOH

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Components

#1: Protein Alpha-ketoglutarate-dependent taurine dioxygenase


Mass: 33682.996 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium avium (bacteria) / Strain: 104 / Gene: MAV_4353 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: A0QKQ0, UniProt: A0A0H2ZSG9*PLUS, taurine dioxygenase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 326 / 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: 2.49 Å3/Da / Density % sol: 50.73 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Internal tracking number 218640E10. PACT screen condition E10: 0.2 M Na/K Phosphate, 20% PEG3350, MyavA.01188.b.A1 PW28977 at 28.9mg/ml. Cryoprotection: 25% ethylene glycol, VAPOR DIFFUSION, ...Details: Internal tracking number 218640E10. PACT screen condition E10: 0.2 M Na/K Phosphate, 20% PEG3350, MyavA.01188.b.A1 PW28977 at 28.9mg/ml. Cryoprotection: 25% ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Feb 22, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.05→41.09 Å / Num. all: 42701 / Num. obs: 42570 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Biso Wilson estimate: 28.296 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 15.84
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique allNum. unique obs% possible all
2.05-2.13.40.4243.1104963124310399.3
2.1-2.160.3423.8114123026100
2.16-2.220.3514.512947296299.3
2.22-2.290.3095.712641281398.5
2.29-2.370.2596.113254275899.8
2.37-2.450.2396.813561270899.9
2.45-2.540.1918.313662261699.9
2.54-2.650.1789.313800249199.9
2.65-2.760.15910.714429240899.9
2.76-2.90.1313.515806229099.8
2.9-3.060.10316.616091222499.9
3.06-3.240.08519.6150342077100
3.24-3.470.06825.714171196899.9
3.47-3.740.05930.213225185499.9
3.74-4.10.04936.111965168999.6
4.1-4.580.03744.2110271542100
4.58-5.290.03544.29808137799.9
5.29-6.480.04368381118299.9
6.48-9.170.03242.86470936100
9.170.02454.8343054698

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å41.09 Å
Translation2.5 Å41.09 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.004data extraction
StructureStudiodata collection
XDSdata reduction
RefinementMethod to determine structure: molecular replacement
Starting model: PDB ENTRY 1OIJ

1oij


Resolution: 2.05→37.78 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.942 / SU B: 7.217 / SU ML: 0.089 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2 2139 5 %RANDOM
Rwork0.171 ---
all0.173 42570 --
obs0.173 42393 99.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.258 Å2
Baniso -1Baniso -2Baniso -3
1-1.04 Å20 Å20 Å2
2---0.15 Å20 Å2
3----0.89 Å2
Refinement stepCycle: LAST / Resolution: 2.05→37.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3832 0 17 326 4175
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0213993
X-RAY DIFFRACTIONr_bond_other_d0.0010.022711
X-RAY DIFFRACTIONr_angle_refined_deg1.3651.9375444
X-RAY DIFFRACTIONr_angle_other_deg0.86936523
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2965497
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.76921.897195
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.55415625
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7961549
X-RAY DIFFRACTIONr_chiral_restr0.0850.2614
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214474
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02875
X-RAY DIFFRACTIONr_mcbond_it0.7021.52444
X-RAY DIFFRACTIONr_mcbond_other0.1951.5989
X-RAY DIFFRACTIONr_mcangle_it1.25223945
X-RAY DIFFRACTIONr_scbond_it2.0731549
X-RAY DIFFRACTIONr_scangle_it3.2694.51491
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 131 -
Rwork0.223 2957 -
all-3088 -
obs--98.88 %
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)
10.6027-0.54280.16011.1447-0.18541.0142-0.1532-0.1042-0.02160.17750.1896-0.04210.11970.0216-0.03640.16250.0662-0.00930.04370.00030.046641.52437.91859.798
21.1362-0.75190.00951.0739-0.12151.5867-0.221-0.3094-0.11990.18440.25870.151-0.0753-0.2152-0.03770.1210.12040.04340.14730.05270.06456.886.84972.301
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 296
2X-RAY DIFFRACTION2B5 - 292

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