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- PDB-2zvq: Crystal structure of mouse cytosolic sulfotransferase mSULT1D1 co... -

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Basic information

Entry
Database: PDB / ID: 2zvq
TitleCrystal structure of mouse cytosolic sulfotransferase mSULT1D1 complex with PAP and alpha-naphthol
ComponentsTyrosine-ester sulfotransferase
KeywordsTRANSFERASE / SULT1D1 / sulfotransferase / naphthol / sulfonation
Function / homology
Function and homology information


Transferases; Transferring sulfur-containing groups; Sulfotransferases / aryl sulfotransferase activity / sulfation / sulfotransferase activity / sulfate assimilation / catecholamine metabolic process / lipid metabolic process / 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
1-NAPHTHOL / ADENOSINE-3'-5'-DIPHOSPHATE / Sulfotransferase 1 family member D1 / Sulfotransferase 1 family member D1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsTeramoto, T. / Sakakibara, Y. / Liu, M.-C. / Suiko, M. / Kimura, M. / Kakuta, Y.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2009
Title: Structural basis for the broad range substrate specificity of a novel mouse cytosolic sulfotransferase--mSULT1D1
Authors: Teramoto, T. / Sakakibara, Y. / Liu, M.-C. / Suiko, M. / Kimura, M. / Kakuta, Y.
History
DepositionNov 14, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 30, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Nov 1, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
X: Tyrosine-ester sulfotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0286
Polymers35,1281
Non-polymers9005
Water7,638424
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)156.178, 67.490, 42.821
Angle α, β, γ (deg.)90.00, 105.47, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11X-2301-

HOH

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Components

#1: Protein Tyrosine-ester sulfotransferase / cytosolic sulfotransferase / mSULT1D1


Mass: 35128.293 Da / Num. of mol.: 1 / Fragment: residues 1-295
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Sult1d1 / Plasmid: pGEX-2TK / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: Q9R2C2, UniProt: Q3UZZ6*PLUS, EC: 2.8.2.9
#2: Chemical ChemComp-A3P / ADENOSINE-3'-5'-DIPHOSPHATE


Type: RNA linking / Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2
#3: Chemical ChemComp-1NP / 1-NAPHTHOL / naphthalen-1-ol


Mass: 144.170 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H8O
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 424 / 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: 3.1 Å3/Da / Density % sol: 60.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 16% PEG 10000, 10mM dithiothreitol, 100mM Bis-Tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Details: mirrors
RadiationMonochromator: Si 111 monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.23→50 Å / Num. all: 96125 / Num. obs: 96125 / % possible obs: 77.6 % / Redundancy: 3.2 % / Biso Wilson estimate: 13.5 Å2 / Rmerge(I) obs: 0.061 / Rsym value: 0.061 / Net I/σ(I): 13.4
Reflection shellHighest resolution: 1.23 Å / Redundancy: 1.2 % / Rmerge(I) obs: 0.743 / Rsym value: 0.743 / % possible all: 9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
BBSdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ZPT

2zpt


Resolution: 1.3→21.41 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.961 / SU B: 0.692 / SU ML: 0.029 / Cross valid method: THROUGHOUT / ESU R: 0.047 / ESU R Free: 0.048 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18819 4677 5 %RANDOM
Rwork0.17137 ---
obs0.17221 89190 89.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.524 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.3→21.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2414 0 61 424 2899
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0222780
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2791.993796
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2165341
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.29924.737133
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.67415528
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5881511
X-RAY DIFFRACTIONr_chiral_restr0.0860.2385
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022119
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.20.21406
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3180.21889
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1060.2365
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2590.261
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.120.236
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6651.51592
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.0622558
X-RAY DIFFRACTIONr_scbond_it1.69631423
X-RAY DIFFRACTIONr_scangle_it2.5674.51209
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.397 116 -
Rwork0.359 2292 -
obs--30.98 %

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