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- PDB-2zpt: Crystal structure of mouse sulfotransferase SULT1D1 complex with PAP -

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Basic information

Entry
Database: PDB / ID: 2zpt
TitleCrystal structure of mouse sulfotransferase SULT1D1 complex with PAP
ComponentsTyrosine-ester sulfotransferase
KeywordsTRANSFERASE / SULT1D1 / catecholamine / sulfotransferase / 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
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: 1.15 Å
AuthorsTeramoto, T. / Sakakibara, Y. / Inada, K. / Liu, M.C. / Suiko, M. / Kimura, M. / Kakuta, Y.
CitationJournal: Febs Lett. / Year: 2008
Title: Crystal structure of mSULT1D1, a mouse catecholamine sulfotransferase
Authors: Teramoto, T. / Sakakibara, Y. / Inada, K. / Kurogi, K. / Liu, M.-C. / Suiko, M. / Kimura, M. / Kakuta, Y.
History
DepositionJul 28, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 18, 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 / pdbx_struct_special_symmetry / 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

Downloads & links

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Assembly

Deposited unit
X: Tyrosine-ester sulfotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6483
Polymers35,1281
Non-polymers5192
Water8,251458
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)155.819, 67.600, 42.696
Angle α, β, γ (deg.)90.00, 105.63, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11X-1266-

HOH

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Components

#1: Protein Tyrosine-ester sulfotransferase


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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 458 / 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: 3.08 Å3/Da / Density % sol: 60.09 %
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: 0.75 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: 0.75 Å / Relative weight: 1
ReflectionResolution: 1.15→50 Å / Num. all: 142203 / Num. obs: 142203 / % possible obs: 94.3 % / Redundancy: 3.4 % / Biso Wilson estimate: 12.4 Å2 / Rmerge(I) obs: 0.044 / Rsym value: 0.044 / Net I/σ(I): 22.3
Reflection shellResolution: 1.15→1.19 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.356 / Mean I/σ(I) obs: 2.1 / Num. unique all: 10387 / Rsym value: 0.356 / % possible all: 69.2

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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 1AQU

1aqu


Resolution: 1.15→20.56 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.971 / SU B: 0.869 / SU ML: 0.019 / Cross valid method: THROUGHOUT / ESU R: 0.03 / ESU R Free: 0.029 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16018 7153 5 %RANDOM
Rwork0.14794 ---
all0.14856 ---
obs0.14856 135033 94.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.432 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.15→20.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2414 0 33 458 2905
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0222824
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2251.9763890
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1895379
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.92925.106141
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.97915556
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0371511
X-RAY DIFFRACTIONr_chiral_restr0.0820.2406
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022176
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.20.21435
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3130.21945
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0940.2381
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2010.249
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1220.238
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7721.51641
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.18122662
X-RAY DIFFRACTIONr_scbond_it1.63831371
X-RAY DIFFRACTIONr_scangle_it2.2384.51180
X-RAY DIFFRACTIONr_rigid_bond_restr0.86433012
X-RAY DIFFRACTIONr_sphericity_free2.8643458
X-RAY DIFFRACTIONr_sphericity_bonded2.44532704
LS refinement shellResolution: 1.15→1.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.25 373 -
Rwork0.246 6928 -
obs--65.77 %

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