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- PDB-3u3k: Crystal structure of hSULT1A1 bound to PAP and 2-Naphtol -

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Basic information

Entry
Database: PDB / ID: 3u3k
TitleCrystal structure of hSULT1A1 bound to PAP and 2-Naphtol
ComponentsSulfotransferase 1A1
KeywordsTRANSFERASE / Arylsulfotransferase / Binding Sites / 2-Naphtol
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 / flavonoid metabolic process / 3'-phosphoadenosine 5'-phosphosulfate metabolic process / sulfation / ethanol catabolic process ...flavonol 3-sulfotransferase activity / aryl sulfotransferase / 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 / amine metabolic process / Paracetamol ADME / estrogen metabolic process / xenobiotic metabolic process / cytosol / cytoplasm
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
naphthalen-2-ol / ADENOSINE-3'-5'-DIPHOSPHATE / Sulfotransferase 1A1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.36 Å
AuthorsGuttman, C. / Berger, I. / Aharoni, A. / Zarivach, R.
CitationJournal: Plos One / Year: 2011
Title: The molecular basis for the broad substrate specificity of human sulfotransferase 1A1.
Authors: Berger, I. / Guttman, C. / Amar, D. / Zarivach, R. / Aharoni, A.
History
DepositionOct 6, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 16, 2011Provider: repository / Type: Initial release
Revision 1.1Apr 11, 2012Group: Database references
Revision 1.2Sep 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)73,9266
Polymers72,7832
Non-polymers1,1434
Water2,036113
1
A: Sulfotransferase 1A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9633
Polymers36,3921
Non-polymers5712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Sulfotransferase 1A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9633
Polymers36,3921
Non-polymers5712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.176, 81.273, 121.760
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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: 36391.664 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Strain: Homo sapiens / Gene: hSULT1A1, OK/SW-cl.88, STP, STP1, SULT1A1 / Plasmid: pET32tr / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / 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: Chemical ChemComp-03V / naphthalen-2-ol / 2-Naphtol


Mass: 144.170 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H8O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 113 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHESE CONFLICTS ARISE FROM POLYMORPHISM OF THE HSULT1A1 GENE (H213). THE CLOSEST SEQUENCE TO THE ...THESE CONFLICTS ARISE FROM POLYMORPHISM OF THE HSULT1A1 GENE (H213). THE CLOSEST SEQUENCE TO THE CRYSTALLIZED SEQUENCE HAS REFERENCE CODE GENBANK: AAI10888.1

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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: 2.45 Å3/Da / Density % sol: 49.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8.5
Details: Tris, Polyethylene glycol 3.350, pH 8.5, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.54 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 1, 2009
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.36→22 Å / Num. obs: 28872 / % possible obs: 94.8 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.089 / Χ2: 1.855 / Net I/σ(I): 11.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.36-2.43.80.4628721.166157.4
2.4-2.444.70.42414171.198195.9
2.44-2.4950.44914651.266197
2.49-2.545.20.41714661.259199.4
2.54-2.65.50.35815071.353199.3
2.6-2.665.60.32114811.3571100
2.66-2.725.70.30315171.4091100
2.72-2.85.70.23214941.478199.9
2.8-2.885.70.21615001.6221100
2.88-2.975.80.19415051.7151100
2.97-3.085.80.16114961.773199.9
3.08-3.25.80.13515191.9441100
3.2-3.355.90.11915112.086199.9
3.35-3.525.90.10415282.2711100
3.52-3.744.30.0949452.833161.9
3.74-4.034.80.08213402.666187.1
4.03-4.435.90.06915272.6281100
4.43-5.075.90.06215632.5321100
5.07-6.365.90.05615732.1571100
6.36-225.40.04816462.181199.3

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1LS6

1ls6


Resolution: 2.36→22 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.929 / WRfactor Rfree: 0.2483 / WRfactor Rwork: 0.1991 / Occupancy max: 1 / Occupancy min: 0.17 / FOM work R set: 0.7644 / SU B: 16.593 / SU ML: 0.191 / SU R Cruickshank DPI: 0.4239 / SU Rfree: 0.281 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.281 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2705 1456 5.1 %RANDOM
Rwork0.2142 ---
obs0.217 28688 95.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 87.37 Å2 / Biso mean: 44.1194 Å2 / Biso min: 19.93 Å2
Baniso -1Baniso -2Baniso -3
1--2.46 Å20 Å20 Å2
2--4.22 Å20 Å2
3----1.77 Å2
Refinement stepCycle: LAST / Resolution: 2.36→22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4709 0 76 113 4898
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0224979
X-RAY DIFFRACTIONr_bond_other_d0.0010.023433
X-RAY DIFFRACTIONr_angle_refined_deg1.6751.9786774
X-RAY DIFFRACTIONr_angle_other_deg0.95638366
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3835587
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.94923.839224
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.71415845
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.0261522
X-RAY DIFFRACTIONr_chiral_restr0.0930.2708
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0215399
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021027
X-RAY DIFFRACTIONr_mcbond_it0.8061.52917
X-RAY DIFFRACTIONr_mcbond_other0.1771.51142
X-RAY DIFFRACTIONr_mcangle_it1.48424755
X-RAY DIFFRACTIONr_scbond_it2.26332062
X-RAY DIFFRACTIONr_scangle_it3.4114.52013
LS refinement shellResolution: 2.361→2.422 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.383 102 -
Rwork0.306 1708 -
all-1810 -
obs--83.14 %
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)
11.9991-0.50970.38080.329-0.07241.12120.0319-0.0509-0.28130.00430.01050.0210.1128-0.0923-0.04240.1202-0.02630.0010.1099-0.00370.137912.3426-5.415-13.3358
21.4894-0.02370.57180.0493-0.08520.9783-0.0014-0.0012-0.06450.0362-0.0123-0.01550.02780.01850.01370.1181-0.0045-0.00790.0801-0.0010.112322.3432-0.305-9.8998
36.2204-0.34210.33441.9415-2.00882.08570.02980.28550.40590.1247-0.02580.0342-0.14440.069-0.0040.1786-0.0156-0.02190.11520.0160.152723.698710.6022-13.5961
41.485-0.61870.18290.67830.87742.5684-0.1279-0.07460.34540.0068-0.0301-0.0498-0.3279-0.29010.1580.15030.0786-0.01040.1288-0.02220.16598.904212.6747-6.5256
51.9303-0.44240.82750.1838-0.09530.8322-0.0913-0.4165-0.12620.11260.08580.0217-0.0472-0.18430.00550.15150.0099-0.00280.18380.02920.046118.22870.32682.2071
612.00356.96512.39444.04171.38930.47770.3913-0.92030.69210.2343-0.53180.39820.073-0.18490.14050.47220.0951-0.18610.1046-0.10990.134722.851215.5787-1.2117
71.5968-0.4833-0.38550.20480.29271.0114-0.00660.01460.183-0.01030.0333-0.0182-0.06480.0656-0.02670.1076-0.01520.00420.13250.01010.126723.700345.4232-33.4791
81.37640.1726-0.75330.13180.05451.3765-0.0192-0.02240.0780.08980.00950.03770.0078-0.05130.00970.1252-0.00680.00950.08970.00170.10849.875842.0925-24.5589
93.94360.21510.13951.82352.23282.7381-0.13150.3316-0.17950.1058-0.00390.10440.1316-0.02350.13540.1607-0.02320.03580.1545-0.01450.074911.546333.8528-32.0819
101.1712-0.2978-0.13710.3214-0.60392.0798-0.2327-0.0304-0.34340.00990.03560.0160.41720.06620.19710.2290.0660.05560.10810.02080.137325.05327.9285-26.0298
110.8781-0.3444-0.18340.16060.22251.1348-0.1197-0.23880.09660.0750.1041-0.02450.10350.20420.01560.13590.0148-0.00990.1456-0.0140.060919.958240.7701-16.7399
124.10170.9227-2.3490.3083-0.73231.7601-0.2832-0.1593-0.62570.00110.0697-0.05440.0358-0.09840.21350.26490.00250.12330.14640.04170.24359.694125.626-23.4592
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 99
2X-RAY DIFFRACTION2A100 - 171
3X-RAY DIFFRACTION3A172 - 181
4X-RAY DIFFRACTION4A182 - 215
5X-RAY DIFFRACTION5A216 - 286
6X-RAY DIFFRACTION6A287 - 295
7X-RAY DIFFRACTION7B8 - 120
8X-RAY DIFFRACTION8B121 - 167
9X-RAY DIFFRACTION9B168 - 180
10X-RAY DIFFRACTION10B181 - 210
11X-RAY DIFFRACTION11B211 - 281
12X-RAY DIFFRACTION12B282 - 295

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