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- PDB-1tex: Mycobacterium smegmatis Stf0 Sulfotransferase with Trehalose -

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Basic information

Entry
Database: PDB / ID: 1tex
TitleMycobacterium smegmatis Stf0 Sulfotransferase with Trehalose
ComponentsStf0 Sulfotransferase
KeywordsTRANSFERASE / mycobacterium / sulfotransferase / sulfolipid / sulfation / trehalose / trehalose-2-sulfate
Function / homology
Function and homology information


transferase activity / carbohydrate metabolic process
Similarity search - Function
Trehalose 2-sulfotransferase / Sulphotransferase Stf0, domain / Stf0 sulphotransferase / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
trehalose / Trehalose 2-sulfotransferase
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsMougous, J.D. / Petzold, C.J. / Senaratne, R.H. / Lee, D.H. / Akey, D.L. / Lin, F.L. / Munchel, S.E. / Pratt, M.R. / Riley, L.W. / Leary, J.A. ...Mougous, J.D. / Petzold, C.J. / Senaratne, R.H. / Lee, D.H. / Akey, D.L. / Lin, F.L. / Munchel, S.E. / Pratt, M.R. / Riley, L.W. / Leary, J.A. / Berger, J.M. / Bertozzi, C.R.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2004
Title: Identification, function and structure of the mycobacterial sulfotransferase that initiates sulfolipid-1 biosynthesis.
Authors: Mougous, J.D. / Petzold, C.J. / Senaratne, R.H. / Lee, D.H. / Akey, D.L. / Lin, F.L. / Munchel, S.E. / Pratt, M.R. / Riley, L.W. / Leary, J.A. / Berger, J.M. / Bertozzi, C.R.
History
DepositionMay 25, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_validate_close_contact / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.src_method / _entity.type
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Feb 14, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Stf0 Sulfotransferase
B: Stf0 Sulfotransferase
C: Stf0 Sulfotransferase
D: Stf0 Sulfotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,3598
Polymers129,9904
Non-polymers1,3694
Water7,386410
1
A: Stf0 Sulfotransferase
B: Stf0 Sulfotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,6804
Polymers64,9952
Non-polymers6852
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4230 Å2
ΔGint-14 kcal/mol
Surface area20550 Å2
MethodPISA
2
C: Stf0 Sulfotransferase
D: Stf0 Sulfotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,6804
Polymers64,9952
Non-polymers6852
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4080 Å2
ΔGint-16 kcal/mol
Surface area20290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.929, 101.929, 228.212
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Detailsthe biological assembly is a dimer: chains A and B form one dimer and chains C and D form a second dimer

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Components

#1: Protein
Stf0 Sulfotransferase


Mass: 32497.508 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (bacteria) / Gene: stf0 / Plasmid: pET28B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: P84151, Transferases; Transferring sulfur-containing groups; Sulfotransferases
#2: Polysaccharide
alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose / trehalose /


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: trehalose
DescriptorTypeProgram
DGlcpa1-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a1-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(1+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 410 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.1 Å3/Da / Density % sol: 60 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: PEG 3000, sodium citrate, trehalose, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1951
2951
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONALS 8.2.211.1
SYNCHROTRONALS 8.3.120.9797, 1.0000
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 41CCDAug 6, 2003mirrors
ADSC QUANTUM 42CCDSep 14, 2003mirrors
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si(111)SINGLE WAVELENGTHMx-ray1
2Si(111)MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.11
20.97971
311
ReflectionResolution: 2.6→50 Å / Num. all: 43904 / Num. obs: 42803 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Rmerge(I) obs: 0.066 / Rsym value: 0.066 / Net I/σ(I): 17.4
Reflection shellResolution: 2.59→2.69 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.409 / Mean I/σ(I) obs: 3.2 / Rsym value: 0.409 / % possible all: 95.6

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.6→15 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.914 / SU B: 29.901 / SU ML: 0.278 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.573 / ESU R Free: 0.324
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
RfactorNum. reflection% reflectionSelection details
Rfree0.27377 2106 5 %RANDOM
Rwork0.21755 ---
obs0.22036 39657 100 %-
all-41763 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 39.957 Å2
Baniso -1Baniso -2Baniso -3
1-2.15 Å21.07 Å20 Å2
2--2.15 Å20 Å2
3----3.22 Å2
Refinement stepCycle: LAST / Resolution: 2.6→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7417 0 92 410 7919
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0217706
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8181.94710573
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6385957
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.88223.199322
X-RAY DIFFRACTIONr_dihedral_angle_3_deg24.791151078
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.3261560
X-RAY DIFFRACTIONr_chiral_restr0.1680.21217
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.025936
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2920.24537
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3390.25319
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2070.2545
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1870.234
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2070.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.381.54924
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.91127761
X-RAY DIFFRACTIONr_scbond_it3.07533219
X-RAY DIFFRACTIONr_scangle_it4.0914.52812
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.665 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.388 154 -
Rwork0.327 2736 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: -37.989 Å / Origin y: -10.5976 Å / Origin z: 19.3212 Å
111213212223313233
T0.2133 Å20.3098 Å2-0.0406 Å2-0.3934 Å20.0183 Å2--0.1336 Å2
L0.4771 °2-0.8672 °2-0.01 °2-2.0153 °2-0.0936 °2--0.0287 °2
S-0.0514 Å °-0.1483 Å °-0.0162 Å °-0.0423 Å °0.1753 Å °0.0989 Å °-0.0738 Å °0.0469 Å °-0.1239 Å °

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