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- PDB-1z29: Crystal Structures of SULT1A2 and SULT1A1*3: Implications in the ... -

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Basic information

Entry
Database: PDB / ID: 1z29
TitleCrystal Structures of SULT1A2 and SULT1A1*3: Implications in the bioactivation of N-hydroxy-2-acetylamino fluorine (OH-AAF)
ComponentsPhenol-sulfating phenol sulfotransferase 2
KeywordsTRANSFERASE / SULT1A2 / PAP / Cation-pi interaction / Plastic substrate binding pocket
Function / homology
Function and homology information


amine biosynthetic process / phenol-containing compound metabolic process / flavonol 3-sulfotransferase activity / aryl sulfotransferase / aryl sulfotransferase activity / Cytosolic sulfonation of small molecules / 3'-phosphoadenosine 5'-phosphosulfate metabolic process / ethanol catabolic process / sulfation / sulfotransferase activity ...amine biosynthetic process / phenol-containing compound metabolic process / flavonol 3-sulfotransferase activity / aryl sulfotransferase / aryl sulfotransferase activity / Cytosolic sulfonation of small molecules / 3'-phosphoadenosine 5'-phosphosulfate metabolic process / ethanol catabolic process / sulfation / sulfotransferase activity / catecholamine metabolic process / steroid metabolic process / 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 / ACETIC ACID / Sulfotransferase 1A2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsLu, J. / Li, H. / Liu, M.C. / Zhang, J. / Li, M. / An, X. / Chang, W.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2010
Title: Crystal structures of SULT1A2 and SULT1A1 *3: insights into the substrate inhibition and the role of Tyr149 in SULT1A2.
Authors: Lu, J. / Li, H. / Zhang, J. / Li, M. / Liu, M.Y. / An, X. / Liu, M.C. / Chang, W.
History
DepositionMar 7, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 30, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 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_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phenol-sulfating phenol sulfotransferase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8704
Polymers34,3431
Non-polymers5273
Water1,00956
1
A: Phenol-sulfating phenol sulfotransferase 2
hetero molecules

A: Phenol-sulfating phenol sulfotransferase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,7408
Polymers68,6852
Non-polymers1,0556
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Unit cell
Length a, b, c (Å)58.398, 65.399, 86.517
Angle α, β, γ (deg.)90.00, 103.69, 90.00
Int Tables number5
Space group name H-MC121
DetailsTHE CRYSTALLOGRAPHIC ASYMMETRIC UNIT CONSISTS OF 1 CHAIN(S). COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN BIOLOGICALLY SIGNIFICANT DIMER STATE Of THE MOLECULE CAN BE GENERATED BY THE TWO FOLD AXIS: -X, Y, -Z.

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Components

#1: Protein Phenol-sulfating phenol sulfotransferase 2 / SULT1A2


Mass: 34342.570 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX-2TK / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P50226, aryl sulfotransferase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#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-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 2.4 Å3/Da / Density % sol: 48.43 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 18% PEG8000, 0.1M Hepes, 0.3M Calcium acetate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 20, 2004
RadiationMonochromator: microfocus / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 12460 / Num. obs: 12460 / % possible obs: 98.9 % / Redundancy: 4.7 % / Biso Wilson estimate: 48.1 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 21.2
Reflection shellResolution: 2.4→2.46 Å / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 3.47 / Num. unique all: 799 / % possible all: 93

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Processing

Software
NameVersionClassification
CrystalCleardata collection
SCALEPACKdata scaling
MOLREPphasing
CNSrefinement
CrystalClear(MSC/RIGAKU)data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LS6

1ls6


Resolution: 2.4→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.253 1241 -random
Rwork0.216 ---
all0.243 12460 --
obs0.243 12007 96 %-
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.33 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2297 0 32 56 2385
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.35
LS refinement shellResolution: 2.4→2.49 Å
RfactorNum. reflection% reflection
Rfree0.337 113 -
Rwork0.273 --
obs-1107 90.2 %

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