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- PDB-7d1x: Crystal structure of 7-alpha-hydroxyl bile acid sulfotransferase ... -

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Basic information

Entry
Database: PDB / ID: 7d1x
TitleCrystal structure of 7-alpha-hydroxyl bile acid sulfotransferase (Sult2a8)
ComponentsSulfotransferase
KeywordsTRANSFERASE / Bile acid / Sulfotransferase / Sult2a8 / 7-hydroxyl
Function / homology
Function and homology information


glycochenodeoxycholate sulfotransferase / bile acid catabolic process / 3'-phosphoadenosine 5'-phosphosulfate binding / sulfotransferase activity / lipid catabolic process / cytosol
Similarity search - Function
Sulfotransferase domain / Sulfotransferase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-3'-5'-DIPHOSPHATE / CHOLIC ACID / Sulfotransferase 2A8
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsAu, W.N.S. / Wang, K.
Citation
Journal: To be published
Title: Crystal structure of sulfotransferase Sult2A8 reveals the distinct mode of substrate binding for sulfonation at 7-hydroxyl group
Authors: Wang, K. / Chan, Y.C. / Lee, S.S.T. / Au, S.W.N.
#1: Journal: Acta Crystallogr., Sect. D: Biol. Crystallogr. / Year: 2012
Title: Identification and characterization of a novel PPAR alpha-regulated and 7-alpha-hydroxyl bile acid-preferring cytosolic sulfotransferase mL-STL (Sult2a8)
Authors: Feng, L. / Yuen, Y.L. / Xu, J. / Liu, X. / Chan, Y.C. / Wang, K. / Fong, W.P. / Cheung, W.T. / Lee, S.S.T.
History
DepositionSep 15, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 22, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sulfotransferase
B: Sulfotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,4726
Polymers66,8012
Non-polymers1,6724
Water1,51384
1
A: Sulfotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2363
Polymers33,4001
Non-polymers8362
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area780 Å2
ΔGint-5 kcal/mol
Surface area13960 Å2
MethodPISA
2
B: Sulfotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2363
Polymers33,4001
Non-polymers8362
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area780 Å2
ΔGint-4 kcal/mol
Surface area12810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.870, 93.870, 71.300
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number77
Space group name H-MP42
Space group name HallP4c
Symmetry operation#1: x,y,z
#2: -y,x,z+1/2
#3: y,-x,z+1/2
#4: -x,-y,z
Components on special symmetry positions
IDModelComponents
11A-641-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 6 through 21 or resid 23...
d_2ens_1(chain "B" and (resid 6 through 21 or resid 23...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1LEUALAA1 - 16
d_12ens_1ILEASPA18 - 29
d_13ens_1ASPASNA31 - 67
d_14ens_1ARGTYRA69 - 79
d_15ens_1ILESERA81 - 84
d_16ens_1LEUPROA90 - 101
d_17ens_1SERASNA103 - 130
d_18ens_1GLULEUA137 - 149
d_19ens_1GLYARGA151 - 221
d_110ens_1ILEILEA226
d_111ens_1PHEPHEA231 - 257
d_112ens_1GLUPHEA259 - 264
d_113ens_1CHDA3PB
d_21ens_1LEUALAC3 - 18
d_22ens_1ILEASPC20 - 31
d_23ens_1ASPASNC33 - 69
d_24ens_1ARGTYRC71 - 81
d_25ens_1ILESERC83 - 86
d_26ens_1LEUPROC88 - 99
d_27ens_1SERLEUC101 - 141
d_28ens_1GLYARGC143 - 213
d_29ens_1ILEILEC215
d_210ens_1PHEPHEC218 - 244
d_211ens_1GLUPHEC246 - 251
d_212ens_1CHDA3PD

NCS oper: (Code: givenMatrix: (-0.00969508060556, 0.999942141646, -0.00466034040359), (0.999952922324, 0.0096931187093, -0.000443380120896), (-0.000398181234895, -0.0046644196116, -0.999989042261) ...NCS oper: (Code: given
Matrix: (-0.00969508060556, 0.999942141646, -0.00466034040359), (0.999952922324, 0.0096931187093, -0.000443380120896), (-0.000398181234895, -0.0046644196116, -0.999989042261)
Vector: -47.5604217049, 46.6109153273, -35.1556341275)

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Components

#1: Protein Sulfotransferase


Mass: 33400.277 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Sult2a8, 2810007J24Rik / Production host: Escherichia coli (E. coli)
References: UniProt: Q8BGL3, Transferases; Transferring sulfur-containing groups; Sulfotransferases
#2: Chemical ChemComp-CHD / CHOLIC ACID


Mass: 408.571 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H40O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-A3P / ADENOSINE-3'-5'-DIPHOSPHATE


Type: RNA linking / Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.58 Å3/Da / Density % sol: 52.24 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: MES, PEG3350, MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Oct 29, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.5→29.68 Å / Num. obs: 21605 / % possible obs: 99 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.157 / Net I/σ(I): 5.6
Reflection shellResolution: 2.5→2.64 Å / Rmerge(I) obs: 0.471 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 3135

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Processing

Software
NameVersionClassification
PHENIXdev_3922refinement
CrystalCleardev_3922data collection
Cootmodel building
SCALEPACKdata scaling
PHENIXphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3F3Y

3f3y


Resolution: 2.5→29.68 Å / Cross valid method: FREE R-VALUE / σ(F): 4.4 / Phase error: 29.7074
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2715 1084 5.02 %
Rwork0.2385 20508 -
obs0.2467 21592 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 55 Å2
Refinement stepCycle: LAST / Resolution: 2.5→29.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4316 0 112 84 4512
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00344553
X-RAY DIFFRACTIONf_angle_d0.72096187
X-RAY DIFFRACTIONf_chiral_restr0.0467673
X-RAY DIFFRACTIONf_plane_restr0.0061784
X-RAY DIFFRACTIONf_dihedral_angle_d11.718657
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 1.66852281149 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.610.33191290.35332551X-RAY DIFFRACTION95.19
2.61-2.750.35811370.3562561X-RAY DIFFRACTION94.92
2.75-2.920.37271330.32722519X-RAY DIFFRACTION94.98
2.92-3.150.3971350.31782563X-RAY DIFFRACTION95
3.15-3.470.291370.2642565X-RAY DIFFRACTION94.93
3.47-3.960.2961320.23212569X-RAY DIFFRACTION95.08
3.97-4.990.21171370.19572564X-RAY DIFFRACTION94.93
4.99-29.680.24371440.20782616X-RAY DIFFRACTION94.51
Refinement TLS params.Method: refined / Origin x: -31.8201183811 Å / Origin y: 15.8113362577 Å / Origin z: -18.1823145926 Å
111213212223313233
T0.556156248035 Å20.184628543091 Å20.0144227862669 Å2-0.342585597422 Å2-0.0156220195375 Å2--0.354838560336 Å2
L0.832372030045 °2-0.593371456203 °20.711320894914 °2-0.776902181305 °2-0.693561477678 °2--0.716173110479 °2
S-0.0137039458317 Å °0.022509967324 Å °-0.164447922175 Å °-0.065691164915 Å °0.0457922409068 Å °0.0251515924342 Å °0.120317650278 Å °0.122951526671 Å °-0.0340837519397 Å °
Refinement TLS groupSelection details: all

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