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- PDB-3bfx: Crystal structure of human sulfotransferase SULT1C1 in complex wi... -

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Basic information

Entry
Database: PDB / ID: 3bfx
TitleCrystal structure of human sulfotransferase SULT1C1 in complex with PAP
ComponentsSulfotransferase 1C2
KeywordsTRANSFERASE / SULFOTRANSFERASE / PAP / STRUCTURAL GENOMICS / PSI / PROTEIN STRUCTURE INITIATIVE / STRUCTURAL GENOMICS CONSORTIUM / SGC / Alternative splicing / Cytoplasm / Polymorphism
Function / homology
Function and homology information


cholesterol sulfotransferase activity / aryl sulfotransferase / aryl sulfotransferase activity / Cytosolic sulfonation of small molecules / sulfation / sulfotransferase activity / amine metabolic process / lysosome / mitochondrion / 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 / Sulfotransferase 1C2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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: Proteins / Year: 2006
Title: Crystal Structures of Human Sulfotransferases Sult1B1 and Sult1C1 Complexed with the Cofactor Product Adenosine-3'-5'-Diphosphate (Pap).
Authors: Dombrovski, L. / Dong, A. / Bochkarev, A. / Plotnikov, A.N.
History
DepositionNov 23, 2007Deposition site: RCSB / Processing site: RCSB
SupersessionDec 4, 2007ID: 2ETG
Revision 1.0Dec 4, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / 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
Revision 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sulfotransferase 1C2
B: Sulfotransferase 1C2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,5644
Polymers69,7102
Non-polymers8542
Water9,224512
1
A: Sulfotransferase 1C2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7093
Polymers34,8551
Non-polymers8542
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Sulfotransferase 1C2


Theoretical massNumber of molelcules
Total (without water)34,8551
Polymers34,8551
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.824, 40.536, 154.612
Angle α, β, γ (deg.)90.00, 91.83, 90.00
Int Tables number3
Space group name H-MP121

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Components

#1: Protein Sulfotransferase 1C2 / Sulfotransferase 1C1 / SULT1C#1 / ST1C2 / humSULTC2


Mass: 34854.875 Da / Num. of mol.: 2 / Mutation: C293S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SULT1C2, SULT1C1 / Plasmid: pET28 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: O00338, Transferases; Transferring sulfur-containing groups; Sulfotransferases
#2: Chemical ChemComp-A3P / ADENOSINE-3'-5'-DIPHOSPHATE


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


Mass: 18.015 Da / Num. of mol.: 512 / 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: 2.19 Å3/Da / Density % sol: 43.93 %
Crystal growTemperature: 297 K / Method: vapor diffusion / pH: 6.5
Details: 1.0M Na Citrate, 0.1M Cacodylate, pH 6.5, VAPOR DIFFUSION, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.97972 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 24, 2005 / Details: Si 111
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97972 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 54077 / Num. obs: 54077 / % possible obs: 95.6 % / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Biso Wilson estimate: 22.4 Å2 / Rmerge(I) obs: 0.042 / Rsym value: 0.042 / Net I/σ(I): 13.4
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.205 / Mean I/σ(I) obs: 4 / Rsym value: 0.205 / % possible all: 70.2

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.2.0005refinement
Coot0.0.33model building
ADSCQuantumdata collection
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1XV1

1xv1
PDB Unreleased entry


Resolution: 1.8→50 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.932 / SU B: 2.702 / SU ML: 0.086 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.129 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Program COOT 0.0.33 also has been used in refinement
RfactorNum. reflection% reflectionSelection details
Rfree0.227 1670 3.1 %RANDOM
Rwork0.183 ---
all0.184 52393 --
obs0.184 52393 95.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.29 Å2
Baniso -1Baniso -2Baniso -3
1-2.02 Å20 Å21.35 Å2
2---0.58 Å20 Å2
3----1.35 Å2
Refinement stepCycle: LAST / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4225 0 54 512 4791
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0224410
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5331.9455967
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7765500
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.60624.253221
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.57915787
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6251522
X-RAY DIFFRACTIONr_chiral_restr0.1110.2603
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023347
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2130.22277
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3120.22993
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.2415
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1930.245
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.130.224
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.11.52601
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.67724099
X-RAY DIFFRACTIONr_scbond_it2.58832140
X-RAY DIFFRACTIONr_scangle_it4.0224.51868
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.85 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 103 -
Rwork0.215 2862 -
obs--71.38 %

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