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- PDB-3qvv: Crystal structure of Ancestral variant b9 of SULT 1A1 in complex ... -

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Basic information

Entry
Database: PDB / ID: 3qvv
TitleCrystal structure of Ancestral variant b9 of SULT 1A1 in complex with PAP and 3-CyC
ComponentsSulfotransferase 1A1
KeywordsTRANSFERASE / aryl sulfotransferase
Function / homology
Function and homology information


aryl sulfotransferase / flavonol 3-sulfotransferase activity / steroid sulfotransferase activity / 3'-phosphoadenosine 5'-phosphosulfate binding / aryl sulfotransferase activity / Cytosolic sulfonation of small molecules / flavonoid metabolic process / 3'-phosphoadenosine 5'-phosphosulfate metabolic process / sulfation / ethanol catabolic process ...aryl sulfotransferase / flavonol 3-sulfotransferase activity / steroid sulfotransferase activity / 3'-phosphoadenosine 5'-phosphosulfate binding / aryl sulfotransferase activity / Cytosolic sulfonation of small molecules / flavonoid metabolic process / 3'-phosphoadenosine 5'-phosphosulfate metabolic process / sulfation / ethanol catabolic process / sulfotransferase activity / catecholamine metabolic process / Paracetamol ADME / amine metabolic process / estrogen metabolic process / xenobiotic metabolic process / cytosol / cytoplasm
Similarity search - Function
Sulfotransferase domain / Sulfotransferase domain / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
7-hydroxy-2-oxo-2H-chromene-3-carbonitrile / ADENOSINE-3'-5'-DIPHOSPHATE / Sulfotransferase 1A1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsAlkolombri, U. / Elias, M. / Tawfik, D.S.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Directed evolution of sulfotransferases and paraoxonases by ancestral libraries.
Authors: Alcolombri, U. / Elias, M. / Tawfik, D.S.
History
DepositionFeb 26, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 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 / 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 / _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: Sulfotransferase 1A1
B: Sulfotransferase 1A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,6616
Polymers68,4332
Non-polymers1,2294
Water64936
1
A: Sulfotransferase 1A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8313
Polymers34,2161
Non-polymers6142
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Sulfotransferase 1A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8313
Polymers34,2161
Non-polymers6142
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)71.790, 71.910, 122.590
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Sulfotransferase 1A1 / ST1A1 / Aryl sulfotransferase 1 / HAST1/HAST2 / Phenol sulfotransferase 1 / Phenol-sulfating phenol ...ST1A1 / Aryl sulfotransferase 1 / HAST1/HAST2 / Phenol sulfotransferase 1 / Phenol-sulfating phenol sulfotransferase 1 / P-PST 1 / ST1A3 / Thermostable phenol sulfotransferase / Ts-PST


Mass: 34216.281 Da / Num. of mol.: 2 / Fragment: SULT1A1 / Mutation: P10Q, M77N, E151D, S168C, V243I, F247I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SULT1A1, STP, STP1, OK/SW-cl.88 / Production host: Escherichia coli (E. coli) / References: UniProt: P50225, aryl sulfotransferase
#2: Chemical ChemComp-A3P / ADENOSINE-3'-5'-DIPHOSPHATE / Adenosine 3',5'-bisphosphate


Type: RNA linking / Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2
#3: Chemical ChemComp-3QV / 7-hydroxy-2-oxo-2H-chromene-3-carbonitrile


Mass: 187.152 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H5NO3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 2.3 Å3/Da / Density % sol: 46.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: The protein was concentrated to 33mg.mL-1. Condition: 18-22% (w/v) PEG 3350 and 50mM Tris-HCL buffer pH 8. Crystals appeared after two days at 293 K. , VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 13, 2011 / Details: Osmic confocal mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.35→50.73 Å / Num. obs: 26722 / % possible obs: 96.9 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 3.61 % / Rsym value: 0.121 / Net I/σ(I): 8.83

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Processing

Software
NameVersionClassification
StructureStudiodata collection
MOLREPphasing
REFMAC5.5.0109refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LS6

1ls6


Resolution: 2.35→46.93 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.925 / SU B: 23.103 / SU ML: 0.246 / Cross valid method: THROUGHOUT / ESU R: 0.488 / ESU R Free: 0.288 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27611 1337 5 %RANDOM
Rwork0.2297 ---
obs0.23203 25385 100 %-
all-15673 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 55.574 Å2
Baniso -1Baniso -2Baniso -3
1--4.29 Å20 Å20 Å2
2--6.76 Å20 Å2
3----2.47 Å2
Refinement stepCycle: LAST / Resolution: 2.35→46.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4700 0 82 36 4818
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0224932
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9471.9796704
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9915574
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.63723.874222
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.70215832
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.941522
X-RAY DIFFRACTIONr_chiral_restr0.0550.2700
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213758
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02998
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0011.52892
X-RAY DIFFRACTIONr_mcbond_other0.0381.51140
X-RAY DIFFRACTIONr_mcangle_it1.72624706
X-RAY DIFFRACTIONr_scbond_it2.82232040
X-RAY DIFFRACTIONr_scangle_it4.194.51998
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.35→2.411 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 100 -
Rwork0.316 1889 -
obs--100 %
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)
17.2978-0.18681.83160.924-0.1895.0212-0.0745-0.3112-0.41970.08210.02610.18510.1216-0.23080.04840.1231-0.00420.0210.01930.00780.16821.135118.238213.5583
26.3522-0.30761.09791.019-0.18884.8591-0.092-0.1324-0.44530.07380.02150.20560.1408-0.18320.07050.1173-0.01550.01910.01020.00240.150831.75453.970813.6811
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 295
2X-RAY DIFFRACTION2B8 - 295

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