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- PDB-3u3r: Crystal structure of D249G mutated Human SULT1A1 bound to PAP and... -

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Basic information

Entry
Database: PDB / ID: 3u3r
TitleCrystal structure of D249G mutated Human SULT1A1 bound to PAP and P-NITROPHENOL
ComponentsSulfotransferase 1A1
KeywordsTRANSFERASE / Arylsulfotransferase / PAP / P-NITROPHENOL / Xenobiotics
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 / SYNCHROTRON / 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 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0394
Polymers36,3341
Non-polymers7053
Water1,802100
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.380, 80.270, 123.160
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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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: 36333.629 Da / Num. of mol.: 1 / Fragment: unp residues 1-295 / Mutation: D249G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Strain: Homo sapiens
Gene: hSULT1A1 D249G mutation, 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-NPO / P-NITROPHENOL


Mass: 139.109 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5NO3
#3: Chemical ChemComp-A3P / ADENOSINE-3'-5'-DIPHOSPHATE


Type: RNA linking / Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 2.46 Å3/Da / Density % sol: 50.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5
Details: Magnesium chloride, BIS-TRIS, Polyethylene glycol 3.350, pH 6.5, vapor diffusion, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 12, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.36→61.58 Å / Num. all: 14032 / Num. obs: 14032 / % possible obs: 92.7 % / Redundancy: 17.1 % / Rsym value: 0.102 / Net I/σ(I): 21.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.36-2.4917.70.34823836221630.348100
2.49-2.6417.60.262.73602120420.26100
2.64-2.8217.70.1793.82587814640.17975.2
2.82-3.0517.50.1335.13176018170.133100
3.05-3.3417.30.0986.42904516750.098100
3.34-3.7316.60.0976.21813510950.09772.2
3.73-4.3116.20.08571884911660.08585.8
4.31-5.2815.60.0698.11809911610.069100
5.28-7.4616.90.0511.7153769080.05100
7.46-53.754150.04412.181225410.04499.4

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Processing

Software
NameVersionClassificationNB
SCALA3.3.15data scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.36→61.58 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.909 / WRfactor Rfree: 0.2129 / WRfactor Rwork: 0.1669 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8683 / SU B: 12.37 / SU ML: 0.14 / SU R Cruickshank DPI: 0.3669 / SU Rfree: 0.2326 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.233 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2167 708 5.1 %RANDOM
Rwork0.1676 ---
obs0.1701 14001 92.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 110.44 Å2 / Biso mean: 31.0541 Å2 / Biso min: 6.34 Å2
Baniso -1Baniso -2Baniso -3
1--2.87 Å20 Å20 Å2
2--4.89 Å20 Å2
3----2.03 Å2
Refinement stepCycle: LAST / Resolution: 2.36→61.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2347 0 47 100 2494
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0222505
X-RAY DIFFRACTIONr_angle_refined_deg1.8461.9783408
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4565295
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.40723.451113
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.53115421
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5941513
X-RAY DIFFRACTIONr_chiral_restr0.1280.2353
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0221921
X-RAY DIFFRACTIONr_mcbond_it0.9331.51461
X-RAY DIFFRACTIONr_mcangle_it1.68622381
X-RAY DIFFRACTIONr_scbond_it2.9531044
X-RAY DIFFRACTIONr_scangle_it4.4274.51024
LS refinement shellResolution: 2.36→2.421 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 51 -
Rwork0.189 1037 -
all-1088 -
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)
13.957-0.36680.09571.04760.18032.8723-0.06650.2128-0.38690.01560.00830.03910.23110.01910.05810.0852-0.03250.00270.0585-0.01570.071515.3647-23.96156.4048
227.4556-1.7382-8.63040.11140.54582.71440.3111-1.87271.6506-0.03130.1704-0.0774-0.06470.5856-0.48150.4199-0.25160.02290.62750.12780.9651-3.7762-28.069417.9164
32.5157-0.09540.52330.64910.02521.592-0.0354-0.0819-0.16810.08090.01390.0770.084-0.07140.02150.0633-0.00250.01040.05280.00280.024417.3611-19.976414.9411
414.6551.20581.65367.31732.22356.710.2584-0.231.1192-0.33680.0518-0.7285-1.05920.6665-0.31030.369-0.0962-0.02540.1683-0.0970.290423.5066-5.434519.6969
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 65
2X-RAY DIFFRACTION2A66 - 72
3X-RAY DIFFRACTION3A73 - 284
4X-RAY DIFFRACTION4A285 - 295

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