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- PDB-5x2b: Crystal structure of mouse sulfotransferase SULT7A1 complexed with PAP -

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Basic information

Entry
Database: PDB / ID: 5x2b
TitleCrystal structure of mouse sulfotransferase SULT7A1 complexed with PAP
Components(Sulfotransferase) x 3
KeywordsTRANSFERASE
Function / homology
Function and homology information


Transferases; Transferring sulfur-containing groups; Sulfotransferases / sulfation / sulfotransferase activity / metal ion binding / 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
ADENOSINE-3'-5'-DIPHOSPHATE / Sulfotransferase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08 Å
AuthorsKanekiyo, M. / Teramoto, T. / Kakuta, Y.
CitationJournal: Pnas Nexus / Year: 2024
Title: A new type of sulfation reaction: C -sulfonation for alpha , beta-unsaturated carbonyl groups by a novel sulfotransferase SULT7A1.
Authors: Kurogi, K. / Sakakibara, Y. / Hashiguchi, T. / Kakuta, Y. / Kanekiyo, M. / Teramoto, T. / Fukushima, T. / Bamba, T. / Matsumoto, J. / Fukusaki, E. / Kataoka, H. / Suiko, M.
History
DepositionJan 31, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 28, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _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_asym_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
Revision 1.2Mar 19, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: Sulfotransferase
A: Sulfotransferase
B: Sulfotransferase
D: Sulfotransferase
E: Sulfotransferase
F: Sulfotransferase
G: Sulfotransferase
H: Sulfotransferase
I: Sulfotransferase
J: Sulfotransferase
K: Sulfotransferase
L: Sulfotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)397,61546
Polymers391,50312
Non-polymers6,11234
Water30,2471679
1
C: Sulfotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1323
Polymers32,6641
Non-polymers4672
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area790 Å2
ΔGint-4 kcal/mol
Surface area13530 Å2
MethodPISA
2
A: Sulfotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1724
Polymers32,6641
Non-polymers5073
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area860 Å2
ΔGint-18 kcal/mol
Surface area13040 Å2
MethodPISA
3
B: Sulfotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2125
Polymers32,6641
Non-polymers5474
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area800 Å2
ΔGint-4 kcal/mol
Surface area12980 Å2
MethodPISA
4
D: Sulfotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0285
Polymers32,4801
Non-polymers5474
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area790 Å2
ΔGint-4 kcal/mol
Surface area12770 Å2
MethodPISA
5
E: Sulfotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1323
Polymers32,6641
Non-polymers4672
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area780 Å2
ΔGint-4 kcal/mol
Surface area13030 Å2
MethodPISA
6
F: Sulfotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1534
Polymers32,5931
Non-polymers5593
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area800 Å2
ΔGint-4 kcal/mol
Surface area13270 Å2
MethodPISA
7
G: Sulfotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1014
Polymers32,5931
Non-polymers5073
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area760 Å2
ΔGint-4 kcal/mol
Surface area12880 Å2
MethodPISA
8
H: Sulfotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0613
Polymers32,5931
Non-polymers4672
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area810 Å2
ΔGint-3 kcal/mol
Surface area13110 Å2
MethodPISA
9
I: Sulfotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1323
Polymers32,6641
Non-polymers4672
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area790 Å2
ΔGint-4 kcal/mol
Surface area13140 Å2
MethodPISA
10
J: Sulfotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1935
Polymers32,5931
Non-polymers5994
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area770 Å2
ΔGint-3 kcal/mol
Surface area12940 Å2
MethodPISA
11
K: Sulfotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1724
Polymers32,6641
Non-polymers5073
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area810 Å2
ΔGint-4 kcal/mol
Surface area13020 Å2
MethodPISA
12
L: Sulfotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1323
Polymers32,6641
Non-polymers4672
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area790 Å2
ΔGint-6 kcal/mol
Surface area13470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)166.174, 81.127, 166.180
Angle α, β, γ (deg.)90.00, 119.95, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 3 types, 12 molecules CABEIKLDFGHJ

#1: Protein
Sulfotransferase


Mass: 32664.318 Da / Num. of mol.: 7 / Fragment: UNP residues 7-287
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Sult6b2, Gm766 / Production host: Escherichia coli (E. coli)
References: UniProt: B7ZWN4, Transferases; Transferring sulfur-containing groups; Sulfotransferases
#2: Protein Sulfotransferase


Mass: 32480.127 Da / Num. of mol.: 1 / Fragment: UNP residues 10-287
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Sult6b2, Gm766 / Production host: Escherichia coli (E. coli)
References: UniProt: B7ZWN4, Transferases; Transferring sulfur-containing groups; Sulfotransferases
#3: Protein
Sulfotransferase


Mass: 32593.240 Da / Num. of mol.: 4 / Fragment: UNP residues 7-287
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Sult6b2, Gm766 / Production host: Escherichia coli (E. coli)
References: UniProt: B7ZWN4, Transferases; Transferring sulfur-containing groups; Sulfotransferases

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Non-polymers , 4 types, 1713 molecules

#4: Chemical
ChemComp-A3P / ADENOSINE-3'-5'-DIPHOSPHATE


Type: RNA linking / Mass: 427.201 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C10H15N5O10P2
#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1679 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationN

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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: 2.48 Å3/Da / Density % sol: 50.38 %
Crystal growTemperature: 294.5 K / Method: vapor diffusion, hanging drop / Details: PEG

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 1, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.907
11H+L, -K, -L20.093
ReflectionResolution: 2.08→50 Å / Num. obs: 229447 / % possible obs: 99.8 % / Redundancy: 3.7 % / Rsym value: 0.085 / Net I/σ(I): 16.8

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.08→50 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.95 / Cross valid method: THROUGHOUT / ESU R Free: 0.039 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23592 11949 5.2 %RANDOM
Rwork0.22074 ---
obs0.22153 217914 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso mean: 33.903 Å2
Baniso -1Baniso -2Baniso -3
1--0.99 Å20 Å22.3 Å2
2---0.8 Å20 Å2
3---1.78 Å2
Refinement stepCycle: 1 / Resolution: 2.08→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms27172 0 356 1679 29207
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.02228412
X-RAY DIFFRACTIONr_bond_other_d00.0219631
X-RAY DIFFRACTIONr_angle_refined_deg1.9491.96738449
X-RAY DIFFRACTIONr_angle_other_deg3.815347791
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.26153375
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.423.9861327
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.383155087
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.36615157
X-RAY DIFFRACTIONr_chiral_restr0.090.24147
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0230937
X-RAY DIFFRACTIONr_gen_planes_other0.0070.025928
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it9.021.516797
X-RAY DIFFRACTIONr_mcbond_other0.0031.56729
X-RAY DIFFRACTIONr_mcangle_it10.946227269
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it11.146311615
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it13.4164.511168
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr10.069348043
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.079→2.133 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.226 873 -
Rwork0.212 15443 -
obs--96.16 %

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