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- PDB-4p06: Bacterial arylsulfate sulfotransferase (ASST) H436N mutant with 4... -

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Basic information

Entry
Database: PDB / ID: 4p06
TitleBacterial arylsulfate sulfotransferase (ASST) H436N mutant with 4-methylumbelliferyl sulfate (MUS) in the active site
ComponentsArylsulfate sulfotransferase AssT
KeywordsTRANSFERASE / sulfotransferase / beta propeller / active site mutant
Function / homology
Function and homology information


aryl-sulfate sulfotransferase / arylsulfate sulfotransferase activity / aryl sulfotransferase activity / periplasmic space
Similarity search - Function
Arylsulphate sulphotransferase monomer, N-terminal domain / Arylsulfotransferase, bacteria / Arylsulfate sulfotransferase AssT, Enterobacteria / Arylsulfotransferase, N-terminal domain / Arylsulfotransferase, N-terminal domain superfamily / Arylsulfotransferase (ASST) / Arylsulfotransferase Ig-like domain / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-MUX / Arylsulfate sulfotransferase AssT / :
Similarity search - Component
Biological speciesEscherichia coli CFT073 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsMalojcic, G. / Owen, R.L. / Glockshuber, R.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Schweizerische Nationalfonds and ETH Zurich in the framework of the NCCR Structural Biology program Switzerland
CitationJournal: Biochemistry / Year: 2014
Title: Structural and mechanistic insights into the PAPS-independent sulfotransfer catalyzed by bacterial aryl sulfotransferase and the role of the DsbL/Dsbl system in its folding.
Authors: Malojcic, G. / Owen, R.L. / Glockshuber, R.
History
DepositionFeb 20, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 26, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 1, 2014Group: Database references
Revision 2.0Sep 27, 2017Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / citation ...atom_site / citation / entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / software / struct_keywords / struct_site / symmetry
Item: _atom_site.pdbx_formal_charge / _citation.journal_id_CSD ..._atom_site.pdbx_formal_charge / _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _software.classification / _struct_keywords.text / _struct_site.details / _symmetry.Int_Tables_number
Revision 2.1Nov 1, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 2.2Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Arylsulfate sulfotransferase AssT
B: Arylsulfate sulfotransferase AssT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,4467
Polymers127,6452
Non-polymers8015
Water28816
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4040 Å2
ΔGint-59 kcal/mol
Surface area42680 Å2
MethodPISA
2
A: Arylsulfate sulfotransferase AssT
B: Arylsulfate sulfotransferase AssT
hetero molecules

A: Arylsulfate sulfotransferase AssT
B: Arylsulfate sulfotransferase AssT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)256,89214
Polymers255,2904
Non-polymers1,60110
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555-y,-x,-z+1/31
Buried area20140 Å2
ΔGint-168 kcal/mol
Surface area73300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)181.533, 181.533, 100.380
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number153
Space group name H-MP3212
DetailsGel filtration confirms the dimerization of the protein in solution

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Components

#1: Protein Arylsulfate sulfotransferase AssT / Aryl sulfotransferase AssT


Mass: 63822.594 Da / Num. of mol.: 2 / Mutation: H463N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli CFT073 (bacteria) / Gene: assT, LF82_506 / Production host: Escherichia coli (E. coli)
References: UniProt: E2QE64, UniProt: A0A0D6H805*PLUS, aryl-sulfate sulfotransferase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-MUX / (4-methyl-2-oxidanylidene-chromen-7-yl) hydrogen sulfate


Mass: 256.232 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H8O6S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.74 Å3/Da / Density % sol: 67.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: sitting drop vapor diffusion method by equilibrating 1.5 ?l of protein solution (22 mg/ml, in 20 mM 4-morpholinepropanesulfonic acid/NaOH pH 7.5, 100 mM NaCl) with 0.5 ?l of reservoir ...Details: sitting drop vapor diffusion method by equilibrating 1.5 ?l of protein solution (22 mg/ml, in 20 mM 4-morpholinepropanesulfonic acid/NaOH pH 7.5, 100 mM NaCl) with 0.5 ?l of reservoir solution consisting of 1.8 M Li2SO4 and 100 mM cacodylic acid/NaOH pH 6.5.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 23, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→52 Å / Num. obs: 109496 / % possible obs: 99.9 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.065 / Rsym value: 0.028 / Net I/σ(I): 13.9
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.84 / Mean I/σ(I) obs: 1.8 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.3_1479)refinement
REFMACrefinement
SCALAdata scaling
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ELQ

3elq


Resolution: 2.1→51.133 Å / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.88 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.1847 5479 5.01 %RANDOM
Rwork0.1631 ---
obs0.1703 109455 99.85 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→51.133 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8890 0 49 16 8955
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0099172
X-RAY DIFFRACTIONf_angle_d1.09212454
X-RAY DIFFRACTIONf_dihedral_angle_d14.6523370
X-RAY DIFFRACTIONf_chiral_restr0.0421328
X-RAY DIFFRACTIONf_plane_restr0.0051630
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1001-2.13630.37272630.32255194X-RAY DIFFRACTION95
2.1363-2.17510.32422800.31075123X-RAY DIFFRACTION95
2.1751-2.2170.32692510.29085238X-RAY DIFFRACTION95
2.217-2.26220.31312660.29065165X-RAY DIFFRACTION95
2.2622-2.31140.30922590.27115207X-RAY DIFFRACTION95
2.3114-2.36520.28092860.24585151X-RAY DIFFRACTION95
2.3652-2.42430.26732620.24735211X-RAY DIFFRACTION95
2.4243-2.48990.26542790.23925185X-RAY DIFFRACTION95
2.4899-2.56310.28612550.23815234X-RAY DIFFRACTION95
2.5631-2.64580.23372440.21675170X-RAY DIFFRACTION95
2.6458-2.74040.24722850.21555192X-RAY DIFFRACTION95
2.7404-2.85010.24212480.20845219X-RAY DIFFRACTION95
2.8501-2.97970.20823100.2055176X-RAY DIFFRACTION94
2.9797-3.13680.2352780.20095193X-RAY DIFFRACTION95
3.1368-3.33320.20152980.18375167X-RAY DIFFRACTION94
3.3332-3.59040.19022880.16815184X-RAY DIFFRACTION95
3.5904-3.95140.16262680.13895190X-RAY DIFFRACTION95
3.9514-4.52250.12812910.11345216X-RAY DIFFRACTION94
4.5225-5.6950.10442860.09675221X-RAY DIFFRACTION94
5.695-39.30990.14412750.12135318X-RAY DIFFRACTION95

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