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

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Basic information

Entry
Database: PDB / ID: 2zyv
TitleCrystal structure of mouse cytosolic sulfotransferase mSULT1D1 complex with PAPS/PAP and p-nitrophenol
ComponentsTyrosine-ester sulfotransferase
KeywordsTRANSFERASE / SULT1D1 / SULT / sulfotransferase / PAPS / p-nitrophenol / Michaelis complex / sulfonation mechanism
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
P-NITROPHENOL / 3'-PHOSPHATE-ADENOSINE-5'-PHOSPHATE SULFATE / 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: 1.81 Å
AuthorsTeramoto, T. / Sakakibara, Y. / Liu, M.-C. / Suiko, M. / Kimura, M. / Kakuta, Y.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2009
Title: Snapshot of a Michaelis complex in a sulfuryl transfer reaction: Crystal structure of a mouse sulfotransferase, mSULT1D1, complexed with donor substrate and accepter substrate
Authors: Teramoto, T. / Sakakibara, Y. / Liu, M.-C. / Suiko, M. / Kimura, M. / Kakuta, Y.
History
DepositionJan 29, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 21, 2009Provider: 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)36,46610
Polymers35,1281
Non-polymers1,3389
Water4,017223
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)155.241, 67.793, 42.904
Angle α, β, γ (deg.)90.00, 105.23, 90.00
Int Tables number5
Space group name H-MC121

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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-PPS / 3'-PHOSPHATE-ADENOSINE-5'-PHOSPHATE SULFATE


Mass: 507.264 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O13P2S
#3: Chemical ChemComp-NPO / P-NITROPHENOL


Mass: 139.109 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5NO3
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 223 / 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: 60.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 16% PEG 10000, 10mM DTT, 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 monochromater / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 38650 / Num. obs: 38650 / % possible obs: 98.4 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.044 / Rsym value: 0.044 / Net I/σ(I): 24.2
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.404 / Mean I/σ(I) obs: 1.9 / Num. unique all: 3709 / Rsym value: 0.404 / % possible all: 94.7

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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: 1.81→21.45 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.01 / SU ML: 0.064 / Cross valid method: THROUGHOUT / ESU R: 0.109 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20254 1940 5 %RANDOM
Rwork0.17855 ---
obs0.17974 36700 98.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.652 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å2-0.01 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.81→21.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2423 0 87 223 2733
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222630
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2551.9823561
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2495304
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.92824.524126
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.93715476
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3561511
X-RAY DIFFRACTIONr_chiral_restr0.0890.2360
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021976
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2010.21332
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.310.21789
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1090.2241
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2620.257
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1380.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7351.51521
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.18722415
X-RAY DIFFRACTIONr_scbond_it1.76631303
X-RAY DIFFRACTIONr_scangle_it2.6994.51138
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.807→1.854 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 141 -
Rwork0.214 2467 -
obs--90.06 %

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