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- PDB-4gra: Crystal structure of SULT1A1 bound with PAP -

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Basic information

Entry
Database: PDB / ID: 4gra
TitleCrystal structure of SULT1A1 bound with PAP
ComponentsSulfotransferase 1A1
KeywordsTRANSFERASE / sulfotransferase / estradiol / hormone regulation
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 / Sulfotransferase 1A1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.56 Å
AuthorsKim, J. / Cook, I. / Wang, T. / Falany, C.N. / Leyh, T.S. / Almo, S.C.
CitationJournal: Biochemistry / Year: 2013
Title: The gate that governs sulfotransferase selectivity.
Authors: Cook, I. / Wang, T. / Almo, S.C. / Kim, J. / Falany, C.N. / Leyh, T.S.
History
DepositionAug 24, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2013Group: Database references
Revision 1.2Feb 13, 2013Group: 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 / 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

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Assembly

Deposited unit
A: Sulfotransferase 1A1
B: Sulfotransferase 1A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,1444
Polymers69,2902
Non-polymers8542
Water1,44180
1
A: Sulfotransferase 1A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0722
Polymers34,6451
Non-polymers4271
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Sulfotransferase 1A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0722
Polymers34,6451
Non-polymers4271
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.296, 122.428, 55.021
Angle α, β, γ (deg.)90.00, 92.12, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.183089, 0.044715, -0.982079), (0.051721, -0.99802, -0.035799), (-0.981735, -0.04424, -0.18504)23.11367, -0.38307, 27.24872

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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: 34644.816 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SULT1A1, STP, STP1, OK/SW-cl.88 / Plasmid: pGEX / Production host: Escherichia coli (E. coli) / References: UniProt: P50225, aryl sulfotransferase
#2: Chemical ChemComp-A3P / ADENOSINE-3'-5'-DIPHOSPHATE


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


Mass: 18.015 Da / Num. of mol.: 80 / 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: 2.35 Å3/Da / Density % sol: 47.57 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1M Tris PH 8.0, 20% PEG, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 25, 2011
RadiationMonochromator: Double silicon(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.56→50 Å / Num. obs: 20267 / % possible obs: 99.8 % / Redundancy: 6 % / Rmerge(I) obs: 0.108 / Net I/σ(I): 15.8
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.355 / Mean I/σ(I) obs: 4.5 / % possible all: 100

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Processing

Software
NameVersionClassification
CBASSdata collection
MOLREPphasing
REFMAC5.7.0025refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2D06

2d06


Resolution: 2.56→48.31 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.866 / SU B: 11.461 / SU ML: 0.257 / Cross valid method: THROUGHOUT / ESU R Free: 0.389 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.26613 913 5.2 %RANDOM
Rwork0.2136 ---
obs0.21633 16784 86.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.669 Å2
Baniso -1Baniso -2Baniso -3
1-1.55 Å20 Å2-2.48 Å2
2---1.72 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.56→48.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4649 0 54 80 4783
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0194853
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2621.9736607
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2585574
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.73223.458214
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.93215791
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5691524
X-RAY DIFFRACTIONr_chiral_restr0.0780.2698
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213704
X-RAY DIFFRACTIONr_gen_planes_other
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.564→2.63 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 45 -
Rwork0.226 751 -
obs--52.86 %

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