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- PDB-3ett: Crystal structure of a bacterial arylsulfate sulfotransferase cat... -

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Basic information

Entry
Database: PDB / ID: 3ett
TitleCrystal structure of a bacterial arylsulfate sulfotransferase catalytic intermediate with 4-nitrophenol bound in the active site
ComponentsArylsulfate sulfotransferase
KeywordsTRANSFERASE / beta propeller / sulfohistidine / protein-substrate complex / periplasm / transesterification / sulfate / phenol / bacteria / transferase 4-nitrophenol / p-nitrophenol / p-nitrophenylsulfate
Function / homology
Function and homology information


aryl-sulfate sulfotransferase / arylsulfate sulfotransferase activity / aryl sulfotransferase activity / periplasmic space / identical protein binding
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
P-NITROPHENOL / : / Arylsulfate sulfotransferase AssT
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsMalojcic, G. / Owen, R.L. / Grimshaw, J.P. / Glockshuber, R.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2008
Title: A structural and biochemical basis for PAPS-independent sulfuryl transfer by aryl sulfotransferase from uropathogenic Escherichia coli.
Authors: Malojcic, G. / Owen, R.L. / Grimshaw, J.P. / Brozzo, M.S. / Dreher-Teo, H. / Glockshuber, R.
History
DepositionOct 8, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 6, 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_conn / struct_ncs_dom_lim / struct_sheet / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_sheet.number_strands / _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: Arylsulfate sulfotransferase
B: Arylsulfate sulfotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,70810
Polymers127,8532
Non-polymers8558
Water13,583754
1
A: Arylsulfate sulfotransferase
B: Arylsulfate sulfotransferase
hetero molecules

A: Arylsulfate sulfotransferase
B: Arylsulfate sulfotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)257,41620
Polymers255,7074
Non-polymers1,70916
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555-x+y,y,-z+2/31
Buried area22940 Å2
ΔGint-181 kcal/mol
Surface area73650 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4730 Å2
ΔGint-70 kcal/mol
Surface area43570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)181.503, 181.503, 99.984
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number153
Space group name H-MP3212
Components on special symmetry positions
IDModelComponents
11A-598-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 4 / Auth seq-ID: 1 - 571 / Label seq-ID: 1 - 571

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

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Components

#1: Protein Arylsulfate sulfotransferase


Mass: 63926.703 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: CFT073 / Gene: ASTA, EcF11_2091 / Plasmid: PDSBA3 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K12
References: UniProt: B3HTA9, UniProt: Q8FDI4*PLUS, aryl-sulfate sulfotransferase
#2: Chemical ChemComp-NPO / P-NITROPHENOL


Mass: 139.109 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5NO3
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 754 / 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: 3.75 Å3/Da / Density % sol: 67.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 1.8M lithium sulfate, 0.1M sodium cacodylate, pH 6.50, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 24, 2008
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 108768 / Num. obs: 108768 / % possible obs: 99.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2.994 / Redundancy: 3.8 % / Biso Wilson estimate: 30.47 Å2 / Rmerge(I) obs: 0.094 / Rsym value: 0.08 / Net I/σ(I): 18.1
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 2.4 / Rsym value: 0.46 / % possible all: 99.6

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Processing

Software
NameVersionClassification
RemDAqdata collection
PHASERphasing
REFMAC5.3refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ELQ

3elq


Resolution: 2.1→33.98 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.936 / SU B: 5.709 / SU ML: 0.142 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.151 / ESU R Free: 0.149
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. PHENIX WAS ALSO USED FOR REFINEMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.232 1769 1.6 %RANDOM
Rwork0.187 ---
all0.188 106194 --
obs0.188 106194 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.37 Å2
Baniso -1Baniso -2Baniso -3
1--2.76 Å2-1.38 Å20 Å2
2---2.76 Å20 Å2
3---4.14 Å2
Refinement stepCycle: LAST / Resolution: 2.1→33.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8919 0 50 754 9723
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0229187
X-RAY DIFFRACTIONr_bond_other_d0.0150.026160
X-RAY DIFFRACTIONr_angle_refined_deg1.6471.94912478
X-RAY DIFFRACTIONr_angle_other_deg1.1643.00115004
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.95151132
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.19124.512441
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.537151499
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9931548
X-RAY DIFFRACTIONr_chiral_restr0.1040.21333
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0210315
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021853
X-RAY DIFFRACTIONr_nbd_refined0.230.21700
X-RAY DIFFRACTIONr_nbd_other0.2230.26746
X-RAY DIFFRACTIONr_nbtor_refined0.1860.24477
X-RAY DIFFRACTIONr_nbtor_other0.0890.24682
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.2614
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2480.230
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2280.285
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1660.224
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.931.56071
X-RAY DIFFRACTIONr_mcbond_other1.0051.52309
X-RAY DIFFRACTIONr_mcangle_it2.08729056
X-RAY DIFFRACTIONr_scbond_it3.44533997
X-RAY DIFFRACTIONr_scangle_it4.3124.53419
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 7510 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
medium positional0.210.5
medium thermal1.362
LS refinement shellResolution: 2.1→2.16 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.36 135 -
Rwork0.293 7807 -
obs--99.41 %

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