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- PDB-3ckl: Crystal structure of human cytosolic sulfotransferase SULT1B1 in ... -

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Basic information

Entry
Database: PDB / ID: 3ckl
TitleCrystal structure of human cytosolic sulfotransferase SULT1B1 in complex with PAP and resveratrol
ComponentsSulfotransferase family cytosolic 1B member 1
KeywordsTRANSFERASE / SULT1B1 / human cytosolic sulfotransferase / resveratrol / SGC / Cytoplasm / Lipid metabolism / Polymorphism / Steroid metabolism / Structural Genomics / Structural Genomics Consortium
Function / homology
Function and homology information


phenol-containing compound metabolic process / biogenic amine metabolic process / aryl sulfotransferase / aryl sulfotransferase activity / Cytosolic sulfonation of small molecules / 3'-phosphoadenosine 5'-phosphosulfate metabolic process / thyroid hormone metabolic process / flavonoid metabolic process / sulfation / sulfotransferase activity ...phenol-containing compound metabolic process / biogenic amine metabolic process / aryl sulfotransferase / 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 / epithelial cell differentiation / 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 / RESVERATROL / Sulfotransferase 1B1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsPan, P.W. / Tempel, W. / Dong, A. / Loppnau, P. / Kozieradzki, I. / Edwards, A.M. / Arrowsmith, C.H. / Weigelt, J. / Bountra, C. / Bochkarev, A. ...Pan, P.W. / Tempel, W. / Dong, A. / Loppnau, P. / Kozieradzki, I. / Edwards, A.M. / Arrowsmith, C.H. / Weigelt, J. / Bountra, C. / Bochkarev, A. / Min, J. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal structure of human cytosolic sulfotransferase SULT1B1 in complex with PAP and resveratrol.
Authors: Pan, P.W. / Tempel, W. / Dong, A. / Loppnau, P. / Kozieradzki, I. / Edwards, A.M. / Arrowsmith, C.H. / Weigelt, J. / Bountra, C. / Bochkarev, A. / Min, J.
History
DepositionMar 16, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 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_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 family cytosolic 1B member 1
B: Sulfotransferase family cytosolic 1B member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,4986
Polymers70,1872
Non-polymers1,3114
Water12,088671
1
A: Sulfotransferase family cytosolic 1B member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7493
Polymers35,0931
Non-polymers6552
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Sulfotransferase family cytosolic 1B member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7493
Polymers35,0931
Non-polymers6552
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.819, 47.613, 92.666
Angle α, β, γ (deg.)90.00, 93.95, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Sulfotransferase family cytosolic 1B member 1 / Sulfotransferase 1B2 / Thyroid hormone sulfotransferase


Mass: 35093.324 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SULT1B1, ST1B2, SULT1B2 / Plasmid: p28a-LIC / Production host: Escherichia coli (E. coli)
Strain (production host): BL21(DE3) codon plus RIL (Stratagene)
References: UniProt: O43704, Transferases; Transferring sulfur-containing groups; Sulfotransferases
#2: Chemical ChemComp-STL / RESVERATROL


Mass: 228.243 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H12O3
#3: Chemical ChemComp-A3P / ADENOSINE-3'-5'-DIPHOSPHATE


Type: RNA linking / Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 671 / 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: 2.47 Å3/Da / Density % sol: 50.23 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 17% PEG 3350, 0.1M Ammonium sulfate, 0.001M DTT, 0.1M Bis-Tris pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.97926 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 28, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.79→50 Å / Num. all: 55786 / Num. obs: 55786 / % possible obs: 85.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 27 Å2 / Rmerge(I) obs: 0.077 / Rsym value: 0.077 / Net I/σ(I): 8.3
Reflection shellResolution: 1.79→1.85 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.545 / Mean I/σ(I) obs: 1.09 / Num. unique all: 1432 / Rsym value: 0.545 / % possible all: 22.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1XV1

1xv1
PDB Unreleased entry


Resolution: 2→19.74 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.913 / SU B: 4.099 / SU ML: 0.118 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.188 / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Program coot 0.3.3 has also been used in refinement
RfactorNum. reflection% reflectionSelection details
Rfree0.24106 2359 5.1 %RANDOM
Rwork0.18107 ---
all0.18418 44063 --
obs0.18418 44063 99.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.293 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2→19.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4842 0 88 671 5601
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0225073
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4541.9696885
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6425587
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.77324.435230
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.72415899
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.8091519
X-RAY DIFFRACTIONr_chiral_restr0.0960.2734
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023801
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2050.22652
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3080.23478
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.2594
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1590.252
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2040.219
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8031.53040
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.324816
X-RAY DIFFRACTIONr_scbond_it2.13932392
X-RAY DIFFRACTIONr_scangle_it3.1984.52069
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 134 -
Rwork0.204 3043 -
obs--94.16 %

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