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- PDB-5hsx: Crystal Structure of a Putative Alpha-ketoglutarate-dependent Tau... -

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Entry
Database: PDB / ID: 5hsx
TitleCrystal Structure of a Putative Alpha-ketoglutarate-dependent Taurine Dioxygenase from Burkholderia xenovorans
ComponentsPutative alpha-ketoglutarate-dependent taurine dioxygenase
KeywordsOXIDOREDUCTASE / SSGCID / dioxygenase / Burkholderia xenovorans / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


2-oxoglutarate-dependent dioxygenase activity / metal ion 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
Alpha-ketoglutarate-dependent taurine dioxygenase
Similarity search - Component
Biological speciesBurkholderia xenovorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal Structure of a Putative Alpha-ketoglutarate-dependent Taurine Dioxygenase from Burkholderia xenovorans
Authors: SSGCID / Dranow, D.M. / Mayclin, S.J. / Lorimer, D. / Edwards, T.E.
History
DepositionJan 26, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 10, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 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_prerelease_seq / pdbx_struct_conn_angle / pdbx_struct_oper_list / 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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_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_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)72,95422
Polymers71,7312
Non-polymers1,22320
Water11,205622
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Putative alpha-ketoglutarate-dependent taurine dioxygenase
hetero molecules

A: Putative alpha-ketoglutarate-dependent taurine dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,95422
Polymers71,7312
Non-polymers1,22320
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area5150 Å2
ΔGint20 kcal/mol
Surface area25040 Å2
MethodPISA
3
B: Putative alpha-ketoglutarate-dependent taurine dioxygenase
hetero molecules

B: Putative alpha-ketoglutarate-dependent taurine dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,95422
Polymers71,7312
Non-polymers1,22320
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area3360 Å2
ΔGint-14 kcal/mol
Surface area23230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.190, 132.600, 55.570
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-790-

HOH

21A-805-

HOH

31B-787-

HOH

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Components

#1: Protein Putative alpha-ketoglutarate-dependent taurine dioxygenase


Mass: 35865.480 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia xenovorans (strain LB400) (bacteria)
Strain: LB400 / Gene: Bxe_A2155 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q13YM5
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 622 / 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: 2.8 Å3/Da / Density % sol: 56.14 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7
Details: BuxeA.00024.i.B1.PS02500 at 24.3 mg/ml, protein was mixed 1:1 with JCSG+(b8): 10% (w/v) PEG-8000, 100 mM Tris base/HCl, pH = 7.0, 200 mM MgCl2, cryoprotected with 20% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 10, 2015 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 75552 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Biso Wilson estimate: 21.63 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.058 / Rrim(I) all: 0.062 / Χ2: 1.007 / Net I/σ(I): 21.52 / Num. measured all: 554951
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.8-1.857.40.4873.7940900551955170.9440.523100
1.85-1.90.3774.8939849536853650.9610.40699.9
1.9-1.950.3046.0538782522952290.9750.327100
1.95-2.010.2357.937890509750950.9810.253100
2.01-2.080.17610.3336714494449440.990.189100
2.08-2.150.14712.3335586478247820.9930.158100
2.15-2.230.12214.6934456463146300.9950.131100
2.23-2.320.10316.9633224446544640.9960.11100
2.32-2.430.08819.6931663424942490.9970.094100
2.43-2.550.0821.8430513409740970.9970.087100
2.55-2.680.06525.6628886388838880.9980.07100
2.68-2.850.05630.2327428370237020.9980.061100
2.85-3.040.04934.6725522348634860.9990.053100
3.04-3.290.04239.7323637326632660.9990.046100
3.29-3.60.03843.7521525300530050.9990.041100
3.6-4.020.03547.1319368272927290.9990.037100
4.02-4.650.03150.417198244824470.9990.033100
4.65-5.690.02950.514538206720670.9990.031100
5.69-8.050.02849.8411376164716470.9990.03100
8.050.02451.0558969719430.9990.02697.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GY9

1gy9


Resolution: 1.8→35.098 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1808 2003 2.65 %
Rwork0.1551 73531 -
obs0.1558 75534 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 109.67 Å2 / Biso mean: 30.9751 Å2 / Biso min: 10.9 Å2
Refinement stepCycle: final / Resolution: 1.8→35.098 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4280 0 82 627 4989
Biso mean--46.56 38.83 -
Num. residues----549
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064521
X-RAY DIFFRACTIONf_angle_d0.8496169
X-RAY DIFFRACTIONf_chiral_restr0.055694
X-RAY DIFFRACTIONf_plane_restr0.006792
X-RAY DIFFRACTIONf_dihedral_angle_d14.8932624
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.7999-1.84490.25031230.218351755298
1.8449-1.89480.21931230.190751935316
1.8948-1.95050.21091520.173651925344
1.9505-2.01350.19631430.165951695312
2.0135-2.08540.19231260.158252335359
2.0854-2.16890.20251590.15451885347
2.1689-2.26760.18321560.149451885344
2.2676-2.38710.18831460.153652205366
2.3871-2.53670.19891610.157652365397
2.5367-2.73250.19431310.159152605391
2.7325-3.00730.16831490.155452555404
3.0073-3.44210.17561270.153753125439
3.4421-4.33550.18241480.139753695517
4.3355-35.10510.14771590.151655415700
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)
12.56310.7434-0.02220.38490.25851.1230.034-0.2627-0.35880.2102-0.17240.21750.5178-0.1998-0.0090.3216-0.17530.07020.2126-0.03030.311731.3744-30.4817-5.8845
22.52551.6044-0.28571.1425-0.43080.3862-0.04120.17330.2562-0.07240.02020.47520.1328-0.14040.04690.2115-0.0601-0.01590.2731-0.06280.332528.1853-14.4977-18.9366
31.090.51440.34450.70680.24320.59360.0785-0.0954-0.05770.1017-0.17770.11160.2238-0.14530.07360.1328-0.06340.01630.1992-0.03310.161540.1054-15.9408-9.0798
40.75930.5204-0.07121.42020.3690.49840.0471-0.0838-0.0158-0.0131-0.17140.18730.1038-0.12350.09090.1124-0.0471-0.00040.2152-0.03120.149640.8455-10.3552-8.2405
52.57271.05821.88523.87692.59432.3393-0.02360.35970.0056-0.4816-0.00950.087-0.4218-0.0370.01380.2207-0.0505-0.00950.247-0.04180.265529.6022-21.1702-22.6535
61.36461.49-0.8154.038-0.26181.470.1174-0.43470.32440.1869-0.25890.6508-0.0222-0.3093-0.01040.1764-0.09810.06530.3689-0.12360.280732.6217-5.7952.8301
73.39970.53290.62157.39133.92214.6416-0.03930.4141-0.4824-0.0688-0.23690.44110.454-0.54030.17210.28-0.03170.00720.2075-0.08760.288343.1235-33.687-32.4049
81.5519-1.0919-0.74241.95370.28411.2686-0.02110.0611-0.408-0.1447-0.07250.020.42350.06560.0540.38440.04650.0350.1346-0.04770.302756.3696-39.5802-34.4841
90.65-0.889-0.38232.68330.4640.4056-0.0755-0.0471-0.09780.11140.0784-0.3950.2450.22940.02650.24440.0987-0.00430.26580.00340.268765.1538-26.2191-23.398
100.6919-0.4192-0.02981.565-0.190.73630.0014-0.0091-0.0834-0.1468-0.0943-0.03790.19660.0280.08770.18390.06060.00910.1445-0.01090.156255.1021-21.6852-31.2523
111.9745-0.59711.00422.6225-0.40922.70940.0058-0.1021-0.18370.1033-0.1538-0.54740.17640.40220.08830.21380.1020.00850.30280.06170.29669.7876-14.3608-33.3872
120.58420.1475-0.23141.7049-0.21560.66260.03720.0343-0.0961-0.0843-0.1416-0.06930.13330.01290.10480.17260.06920.01050.1579-0.00090.153155.9632-17.3338-31.1403
133.0106-0.0879-0.45152.9061-0.58830.1922-0.0978-0.7591-0.09520.8057-0.1039-0.02090.10490.45310.16620.51690.04880.02060.36430.00450.244860.4985-32.3762-17.2425
142.0938-0.9830.20670.91960.20460.2230.10460.4695-0.0302-0.6022-0.2924-0.32340.1221-0.0417-0.02260.32130.1680.09140.22950.02480.20763.9709-18.0254-45.3732
153.2325-0.83881.35215.3127-4.24186.0879-0.2043-0.5383-0.38180.45570.2386-1.02881.31450.51180.09470.70050.24110.05160.5557-0.00790.611773.8994-22.3806-32.0265
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 11 through 82 )A11 - 82
2X-RAY DIFFRACTION2chain 'A' and (resid 83 through 112 )A83 - 112
3X-RAY DIFFRACTION3chain 'A' and (resid 113 through 164 )A113 - 164
4X-RAY DIFFRACTION4chain 'A' and (resid 165 through 266 )A165 - 266
5X-RAY DIFFRACTION5chain 'A' and (resid 267 through 285 )A267 - 285
6X-RAY DIFFRACTION6chain 'A' and (resid 286 through 306 )A286 - 306
7X-RAY DIFFRACTION7chain 'B' and (resid 11 through 26 )B11 - 26
8X-RAY DIFFRACTION8chain 'B' and (resid 27 through 80 )B27 - 80
9X-RAY DIFFRACTION9chain 'B' and (resid 81 through 118 )B81 - 118
10X-RAY DIFFRACTION10chain 'B' and (resid 119 through 164 )B119 - 164
11X-RAY DIFFRACTION11chain 'B' and (resid 165 through 197 )B165 - 197
12X-RAY DIFFRACTION12chain 'B' and (resid 198 through 266 )B198 - 266
13X-RAY DIFFRACTION13chain 'B' and (resid 267 through 285 )B267 - 285
14X-RAY DIFFRACTION14chain 'B' and (resid 286 through 298 )B286 - 298
15X-RAY DIFFRACTION15chain 'B' and (resid 299 through 315 )B299 - 315

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