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- PDB-2ad1: Human Sulfotransferase SULT1C2 -

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Basic information

Entry
Database: PDB / ID: 2ad1
TitleHuman Sulfotransferase SULT1C2
ComponentsSulfotransferase 1C2
KeywordsTRANSFERASE / x-ray crystallography / sulfate conjugation / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


aryl sulfotransferase / aryl sulfotransferase activity / Cytosolic sulfonation of small molecules / flavonoid metabolic process / 3'-phosphoadenosine 5'-phosphosulfate metabolic process / sulfation / sulfotransferase activity / ethanol catabolic process / Paracetamol ADME / doxorubicin metabolic process ...aryl sulfotransferase / aryl sulfotransferase activity / Cytosolic sulfonation of small molecules / flavonoid metabolic process / 3'-phosphoadenosine 5'-phosphosulfate metabolic process / sulfation / sulfotransferase activity / ethanol catabolic process / Paracetamol ADME / doxorubicin 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
Sulfotransferase 1C4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsDong, A. / Dombrovski, L. / Loppnau, P. / Edwards, A.M. / Arrowsmith, C.H. / Weigelt, J. / Sundstrom, M. / Bochkarev, A. / Plotnikov, A.N. / Structural Genomics Consortium (SGC)
CitationJournal: Plos Biol. / Year: 2007
Title: Structural and chemical profiling of the human cytosolic sulfotransferases.
Authors: Allali-Hassani, A. / Pan, P.W. / Dombrovski, L. / Najmanovich, R. / Tempel, W. / Dong, A. / Loppnau, P. / Martin, F. / Thornton, J. / Thonton, J. / Edwards, A.M. / Bochkarev, A. / Plotnikov, ...Authors: Allali-Hassani, A. / Pan, P.W. / Dombrovski, L. / Najmanovich, R. / Tempel, W. / Dong, A. / Loppnau, P. / Martin, F. / Thornton, J. / Thonton, J. / Edwards, A.M. / Bochkarev, A. / Plotnikov, A.N. / Vedadi, M. / Arrowsmith, C.H.
History
DepositionJul 19, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 2, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sulfotransferase 1C2


Theoretical massNumber of molelcules
Total (without water)35,0201
Polymers35,0201
Non-polymers00
Water2,756153
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.824, 58.824, 189.287
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Cell settingtrigonal
Space group name H-MP3221

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Components

#1: Protein Sulfotransferase 1C2 / E.C.2.8.2.- / SULT1C2 / SULT1C#2


Mass: 35020.141 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SULT1C2 / Plasmid: pET28 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: O75897, Transferases; Transferring sulfur-containing groups; Sulfotransferases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / 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: 2.7 Å3/Da / Density % sol: 54.7 %
Crystal growTemperature: 300 K / Method: vapor diffusion / pH: 4.6
Details: 20%PEG 3350, 0.2M Li citracte pH4.6, VAPOR DIFFUSION, temperature 300K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 29, 2005 / Details: VeriMax
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 25032 / Num. obs: 25032 / % possible obs: 93.7 % / Observed criterion σ(I): 0 / Redundancy: 10.7 % / Biso Wilson estimate: 37.4 Å2 / Rmerge(I) obs: 0.059 / Rsym value: 0.059 / Net I/σ(I): 14.6
Reflection shellResolution: 2→2.07 Å / Redundancy: 9.5 % / Rmerge(I) obs: 0.767 / Mean I/σ(I) obs: 2.89 / Num. unique all: 1881 / Rsym value: 0.767 / % possible all: 72.5

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Processing

Software
NameVersionClassification
CrystalCleardata collection
HKL-2000data reduction
PHASERphasing
REFMAC5.2refinement
Omodel building
ARP/wARPmodel building
CrystalClear(MSC/RIGAKU)data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZHE

1zhe
PDB Unreleased entry


Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.931 / SU B: 4.143 / SU ML: 0.117 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.174 / ESU R Free: 0.166 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26166 1264 5 %RANDOM
Rwork0.21774 ---
all0.21993 23766 --
obs0.21993 23766 94.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.747 Å2
Baniso -1Baniso -2Baniso -3
1-0.79 Å20.39 Å20 Å2
2--0.79 Å20 Å2
3----1.18 Å2
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2051 0 0 153 2204
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0222113
X-RAY DIFFRACTIONr_angle_refined_deg1.7031.942853
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9075240
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.71224.158101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.69915388
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.703158
X-RAY DIFFRACTIONr_chiral_restr0.1190.2296
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021583
X-RAY DIFFRACTIONr_nbd_refined0.2330.21007
X-RAY DIFFRACTIONr_nbtor_refined0.3090.21385
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1990.2145
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2090.234
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1280.214
X-RAY DIFFRACTIONr_mcbond_it1.2881.51262
X-RAY DIFFRACTIONr_mcangle_it2.0921981
X-RAY DIFFRACTIONr_scbond_it2.96331011
X-RAY DIFFRACTIONr_scangle_it4.4164.5872
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 68 -
Rwork0.277 1250 -
obs--69.15 %

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