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

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Basic information

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


flavonol 3-sulfotransferase activity / aryl sulfotransferase / steroid sulfotransferase activity / 3'-phosphoadenosine 5'-phosphosulfate binding / aryl sulfotransferase activity / Cytosolic sulfonation of small molecules / 3'-phosphoadenosine 5'-phosphosulfate metabolic process / thyroid hormone metabolic process / flavonoid metabolic process / sulfation ...flavonol 3-sulfotransferase activity / aryl sulfotransferase / steroid sulfotransferase activity / 3'-phosphoadenosine 5'-phosphosulfate binding / aryl sulfotransferase activity / Cytosolic sulfonation of small molecules / 3'-phosphoadenosine 5'-phosphosulfate metabolic process / thyroid hormone metabolic process / flavonoid metabolic process / sulfation / sulfotransferase activity / ethanol catabolic process / dopamine catabolic process / amine metabolic process / Paracetamol ADME / estrogen metabolic process / xenobiotic metabolic process / cytoplasm / cytosol
Similarity search - Function
Sulfotransferase domain / Sulfotransferase domain / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-3'-5'-DIPHOSPHATE / P-NITROPHENOL / Sulfotransferase 1A1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsAlcolombri, 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)69,6898
Polymers68,4332
Non-polymers1,2576
Water1,56787
1
A: Sulfotransferase 1A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8454
Polymers34,2161
Non-polymers6283
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Sulfotransferase 1A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8454
Polymers34,2161
Non-polymers6283
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.860, 71.540, 122.770
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 / 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-NPO / P-NITROPHENOL


Mass: 139.109 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5NO3
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-A3P / ADENOSINE-3'-5'-DIPHOSPHATE


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


Mass: 18.015 Da / Num. of mol.: 87 / 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: 2.15 Å3/Da / Density % sol: 42.66 %
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 10, 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: 2.5→48.85 Å / Num. all: 21070 / Num. obs: 20787 / % possible obs: 97.8 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 4.91 % / Rsym value: 0.126 / Net I/σ(I): 10.62

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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: 2.5→48.85 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.908 / SU B: 9.613 / SU ML: 0.216 / Cross valid method: THROUGHOUT / ESU R Free: 0.314 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24712 1040 5 %RANDOM
Rwork0.20835 ---
obs0.21029 19746 100 %-
all-21070 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.119 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0.05 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 2.5→48.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4702 0 82 87 4871
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0224987
X-RAY DIFFRACTIONr_bond_other_d0.0010.023421
X-RAY DIFFRACTIONr_angle_refined_deg0.5871.9766785
X-RAY DIFFRACTIONr_angle_other_deg1.1413.0018313
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.8135588
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.67123.894226
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.05915840
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.2891522
X-RAY DIFFRACTIONr_chiral_restr0.0390.2712
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0215438
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021017
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_it0.7751.52922
X-RAY DIFFRACTIONr_mcbond_other0.1151.51146
X-RAY DIFFRACTIONr_mcangle_it1.44424764
X-RAY DIFFRACTIONr_scbond_it2.35232065
X-RAY DIFFRACTIONr_scangle_it3.7134.52017
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 77 -
Rwork0.249 1452 -
obs--100 %

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