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- PDB-2h8k: Human Sulfotranferase SULT1C3 in complex with PAP -

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Basic information

Entry
Database: PDB / ID: 2h8k
TitleHuman Sulfotranferase SULT1C3 in complex with PAP
ComponentsSULT1C3 splice variant d
KeywordsTRANSFERASE / sulfotransferase / SULFATE CONJUGATION / PAP / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


alcohol sulfotransferase activity / bile-salt sulfotransferase activity / alcohol sulfotransferase / aryl sulfotransferase / 3'-phosphoadenosine 5'-phosphosulfate binding / aryl sulfotransferase activity / 3'-phosphoadenosine 5'-phosphosulfate metabolic process / sulfation / sulfur compound metabolic process / xenobiotic metabolic process ...alcohol sulfotransferase activity / bile-salt sulfotransferase activity / alcohol sulfotransferase / aryl sulfotransferase / 3'-phosphoadenosine 5'-phosphosulfate binding / aryl sulfotransferase activity / 3'-phosphoadenosine 5'-phosphosulfate metabolic process / sulfation / sulfur compound metabolic process / xenobiotic metabolic process / cholesterol metabolic process / lipid metabolic process / 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 1C3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsTempel, W. / Dombrovski, L. / Loppnau, P. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Plotnikov, A.N. / Structural Genomics Consortium (SGC)
Citation
Journal: Plos Biol. / Year: 2007
Title: Structural and chemical profiling of the human cytosolic sulfotransferases.
Authors: Allali-Hassani, A. / Pan, P.W. / Dombrovski, L. / Najmanovich, R. / Tempel, W. / Dong, A. / Loppnau, P. / Martin, F. / Thornton, J. / Thonton, J. / Edwards, A.M. / Bochkarev, A. / Plotnikov, ...Authors: Allali-Hassani, A. / Pan, P.W. / Dombrovski, L. / Najmanovich, R. / Tempel, W. / Dong, A. / Loppnau, P. / Martin, F. / Thornton, J. / Thonton, J. / Edwards, A.M. / Bochkarev, A. / Plotnikov, A.N. / Vedadi, M. / Arrowsmith, C.H.
#1: Journal: FEBS Lett. / Year: 2001
Title: The dimerization motif of cytosolic sulfotransferases.
Authors: Petrotchenko, E.V. / Pedersen, L.C. / Borchers, C.H. / Tomer, K.B. / Negishi, M.
History
DepositionJun 7, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 20, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Aug 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_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _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

Downloads & links

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Assembly

Deposited unit
A: SULT1C3 splice variant d
B: SULT1C3 splice variant d
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,0264
Polymers72,1712
Non-polymers8542
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.161, 108.717, 136.925
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: PHE / Beg label comp-ID: PHE / End auth comp-ID: A3P / End label comp-ID: A3P / Refine code: 1 / Auth seq-ID: 18 - 401 / Label seq-ID: 20

Dom-IDAuth asym-IDLabel asym-ID
1AA - C
2BB - D

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Components

#1: Protein SULT1C3 splice variant d


Mass: 36085.746 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SULT1C3 / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q6IMI6, 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

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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: 2.25 Å3/Da / Density % sol: 45.24 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.9
Details: PAP, 18% PEG-3350, 0.2M ammonium formate, BisTris, pH 6.9, vapor diffusion, sitting drop, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 19, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→100 Å / Num. obs: 13470 / % possible obs: 98.4 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.149 / Χ2: 1.123 / Net I/σ(I): 10.5
Reflection shell
Resolution (Å)% possible obs (%)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2
3-3.1187.940.65111820.919
3.11-3.2398.74.90.5913340.783
3.23-3.3899.85.70.4913390.716
3.38-3.5699.95.90.38513500.842
3.56-3.781005.90.31713551.132
3.78-4.0799.960.24513511.114
4.07-4.481006.10.16513600.868
4.48-5.1399.96.10.13113801.148
5.13-6.461006.20.10913891.415
6.46-10097.75.90.06714302.039

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation3.2 Å28.97 Å
Translation3.2 Å28.97 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefmac_5.2.0019refinement
PDB_EXTRACT1.701data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2AD1

2ad1


Resolution: 3.2→30 Å / Cor.coef. Fo:Fc: 0.875 / Cor.coef. Fo:Fc free: 0.815 / WRfactor Rfree: 0.375 / WRfactor Rwork: 0.32 / SU B: 34 / SU ML: 0.609 / ESU R Free: 0.654 / Details: Molprobity was also used for the refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.3424 440 4.027 %thin shells
Rwork0.2917 ---
all0.294 ---
obs-10927 99.039 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 57.491 Å2
Baniso -1Baniso -2Baniso -3
1--0.6 Å20 Å20 Å2
2---3.632 Å20 Å2
3---4.232 Å2
Refinement stepCycle: LAST / Resolution: 3.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3564 0 54 0 3618
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0213736
X-RAY DIFFRACTIONr_angle_refined_deg1.391.9485138
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7315486
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.24923.281128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.39215452
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.846156
X-RAY DIFFRACTIONr_chiral_restr0.0760.2570
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022868
X-RAY DIFFRACTIONr_nbd_refined0.2490.21949
X-RAY DIFFRACTIONr_nbtor_refined0.3120.22606
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.2185
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2070.213
X-RAY DIFFRACTIONr_mcbond_it0.3961.52491
X-RAY DIFFRACTIONr_mcangle_it0.72623842
X-RAY DIFFRACTIONr_scbond_it0.6931501
X-RAY DIFFRACTIONr_scangle_it1.1164.51296
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1809 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
TIGHT POSITIONAL0.0370.05
TIGHT THERMAL0.0560.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection all% reflection obs (%)
3.2-3.28200.3057880.30579299.495
3.282-3.3710.364550.2917110.297766100
3.371-3.4670.4550.3036950.30975699.206
3.467-3.57300.3247380.324738100
3.573-3.6880.379550.3946380.39371596.923
3.688-3.81500.3086660.30867998.085
3.815-3.9570.352550.3175800.31966994.918
3.957-4.11600.2856540.28565799.543
4.116-4.2950.33550.2695580.275613100
4.295-4.500.2595780.25958299.313
4.5-4.73700.2545710.25457399.651
4.737-5.0170.301550.2864910.288546100
5.017-5.35300.35070.3507100
5.353-5.7660.483550.2954230.314478100
5.766-6.29300.344450.34445100
6.293-6.99800.3114120.311412100
6.998-8.00800.3223570.322357100
8.008-9.6380.265550.2192580.226313100
9.638-12.97700.2142550.21425898.837
12.977-3000.331620.3317791.525

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