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- PDB-1q1q: Crystal structure of human pregnenolone sulfotransferase (SULT2B1... -

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Basic information

Entry
Database: PDB / ID: 1q1q
TitleCrystal structure of human pregnenolone sulfotransferase (SULT2B1a) in the presence of PAP
Componentssulfotransferase family, cytosolic, 2B, member 1 isoform a
KeywordsTRANSFERASE / sulfotransferase / pregnenolone / SULT2B1 / PAP
Function / homology
Function and homology information


cholesterol sulfotransferase activity / alcohol sulfotransferase / steroid sulfotransferase activity / Cytosolic sulfonation of small molecules / 3'-phosphoadenosine 5'-phosphosulfate metabolic process / sulfation / steroid hormone binding / cholesterol binding / positive regulation of epidermal cell differentiation / small molecule binding ...cholesterol sulfotransferase activity / alcohol sulfotransferase / steroid sulfotransferase activity / Cytosolic sulfonation of small molecules / 3'-phosphoadenosine 5'-phosphosulfate metabolic process / sulfation / steroid hormone binding / cholesterol binding / positive regulation of epidermal cell differentiation / small molecule binding / steroid metabolic process / cholesterol metabolic process / nucleic acid binding / negative regulation of cell population proliferation / intracellular membrane-bounded organelle / endoplasmic reticulum / extracellular exosome / nucleus / 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 2B1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.91 Å
AuthorsLee, K.A. / Fuda, H. / Lee, Y.C. / Negishi, M. / Strott, C.A. / Pedersen, L.C.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Crystal structure of human cholesterol sulfotransferase (SULT2B1b) in the presence of pregnenolone and 3'-phosphoadenosine 5'-phosphate. Rationale for specificity differences between ...Title: Crystal structure of human cholesterol sulfotransferase (SULT2B1b) in the presence of pregnenolone and 3'-phosphoadenosine 5'-phosphate. Rationale for specificity differences between prototypical SULT2A1 and the SULT2BG1 isoforms.
Authors: Lee, K.A. / Fuda, H. / Lee, Y.C. / Negishi, M. / Strott, C.A. / Pedersen, L.C.
History
DepositionJul 22, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 11, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Aug 16, 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_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 350BIOLOGICAL UNIT UNKNOWN

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: sulfotransferase family, cytosolic, 2B, member 1 isoform a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5115
Polymers39,6461
Non-polymers8654
Water1267
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.244, 75.244, 252.246
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Detailsnot known

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Components

#1: Protein sulfotransferase family, cytosolic, 2B, member 1 isoform a / SULT2B1a


Mass: 39645.871 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SULT2B1 / Plasmid: PGEX-6P-3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: O00204
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-A3P / ADENOSINE-3'-5'-DIPHOSPHATE


Type: RNA linking / Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2
#4: Chemical ChemComp-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES


Mass: 207.290 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H17NO3S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 4.5 Å3/Da / Density % sol: 72.66 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 0.8M sodium tartrate, 0.2M Li2So4, 0.1M CHES, 4mM PAP, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
115 mg/mlprotein1drop
225 mMTris1droppH7.5
3100 mM1dropNaCl
40.8-1.0 Msodium tartrate1reservoir
50.2 M1reservoirLi2SO4
60.1 MCHES1reservoirpH9.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 5, 2001 / Details: MSC Yale mirrors
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.9→25 Å / Num. obs: 29928 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 80.5 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 12.1
Reflection shellResolution: 2.9→3 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.598 / Mean I/σ(I) obs: 2.1 / Num. unique all: 2991 / % possible all: 98.5
Reflection
*PLUS
Lowest resolution: 25 Å / % possible obs: 99 % / Num. measured all: 105367
Reflection shell
*PLUS
% possible obs: 98.5 %

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Processing

Software
NameVersionClassification
CNS1refinement
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EFH

1efh


Resolution: 2.91→21.94 Å / Rfactor Rfree error: 0.007 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.269 1401 4.9 %RANDOM
Rwork0.249 ---
all0.25 29895 --
obs0.249 28494 94.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 15.3004 Å2 / ksol: 0.294595 e/Å3
Displacement parametersBiso mean: 46.3 Å2
Baniso -1Baniso -2Baniso -3
1-4.09 Å20 Å20 Å2
2--4.09 Å20 Å2
3----8.17 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.5 Å0.45 Å
Luzzati d res low-5 Å
Luzzati sigma a0.76 Å0.74 Å
Refinement stepCycle: LAST / Resolution: 2.91→21.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2189 0 54 7 2250
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d22
X-RAY DIFFRACTIONc_improper_angle_d1.18
X-RAY DIFFRACTIONc_mcbond_it0.971.5
X-RAY DIFFRACTIONc_mcangle_it1.72
X-RAY DIFFRACTIONc_scbond_it1.272
X-RAY DIFFRACTIONc_scangle_it2.12.5
LS refinement shellResolution: 2.9→3.08 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.406 192 4.8 %
Rwork0.41 3804 -
obs--78.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2PAP.PARPAP.TOP
X-RAY DIFFRACTION3NHE.PARION.TOP
X-RAY DIFFRACTION4WATER_REP.PARAMNHE.TOP
X-RAY DIFFRACTION5ION.PARAMWATER.TOP
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.8
LS refinement shell
*PLUS
Rfactor Rfree: 0.41 / Rfactor Rwork: 0.41

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