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- PDB-4p07: Bacterial aryl sulfotransferase (ASST) soaked with human urine -

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Basic information

Entry
Database: PDB / ID: 4p07
TitleBacterial aryl sulfotransferase (ASST) soaked with human urine
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
Arylsulfate sulfotransferase AssT / :
Similarity search - Component
Biological speciesEscherichia coli CFT073 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å
AuthorsMalojcic, G. / Owen, R.L. / Glockshuber, R.
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 1.2Sep 27, 2017Group: Advisory / Database references ...Advisory / Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms / software / struct_keywords
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _software.classification / _struct_keywords.text
Revision 1.3Nov 1, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.4Sep 27, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein
Revision 1.5Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)127,8854
Polymers127,6932
Non-polymers1922
Water3,819212
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3860 Å2
ΔGint-47 kcal/mol
Surface area42980 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)255,7718
Polymers255,3874
Non-polymers3844
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_755-x+y+2,y,-z+2/31
Buried area20220 Å2
ΔGint-151 kcal/mol
Surface area73460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)182.295, 182.295, 101.592
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number153
Space group name H-MP3212
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.958483, -0.001255, 0.285147), (0.000836, -0.999998, -0.001591), (0.285149, -0.001287, 0.958482)347.44714, 109.16171, -50.47245
DetailsGel filtration confirms the dimerization of the protein in solution

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Components

#1: Protein Arylsulfate sulfotransferase AssT / Aryl sulfotransferase AssT


Mass: 63846.641 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


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 212 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.82 Å3/Da / Density % sol: 67.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
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: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 10, 2008
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.59→48.4 Å / Num. obs: 58584 / % possible obs: 98.2 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.103 / Rsym value: 0.13 / Net I/σ(I): 9.8
Reflection shellResolution: 2.59→2.66 Å / Redundancy: 4.1 % / Rmerge(I) obs: 1.035 / Mean I/σ(I) obs: 1.7 / % possible all: 91.4

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
PHENIXrefinement
SCALAdata scaling
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ELQ

3elq


Resolution: 2.59→48.4 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.927 / SU B: 9.447 / SU ML: 0.194 / Cross valid method: THROUGHOUT / ESU R: 0.335 / ESU R Free: 0.242 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.224 2945 5 %RANDOM
Rwork0.18 ---
obs0.183 55613 98.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.67 Å2
Baniso -1Baniso -2Baniso -3
1--2.36 Å2-2.36 Å20 Å2
2---2.36 Å20 Å2
3---7.66 Å2
Refinement stepCycle: 1 / Resolution: 2.59→48.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8975 0 10 212 9197
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0199224
X-RAY DIFFRACTIONr_bond_other_d0.0070.028595
X-RAY DIFFRACTIONr_angle_refined_deg1.8061.94512532
X-RAY DIFFRACTIONr_angle_other_deg1.18319793
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.26151142
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.58624.562445
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.688151515
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4511548
X-RAY DIFFRACTIONr_chiral_restr0.0930.21351
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02110561
X-RAY DIFFRACTIONr_gen_planes_other0.0040.022131
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.59→2.66 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.412 216 -
Rwork0.354 3796 -
obs--91.58 %

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