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- PDB-3f5f: Crystal structure of heparan sulfate 2-O-sulfotransferase from ga... -

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Basic information

Entry
Database: PDB / ID: 3f5f
TitleCrystal structure of heparan sulfate 2-O-sulfotransferase from gallus gallus as a maltose binding protein fusion.
ComponentsMaltose-binding periplasmic protein, Heparan sulfate 2-O-sulfotransferase 1
KeywordsTransport / Transferase / maltose binding protein / fusion / heparan sulfate biosynthesis / sulfotransferase / Glycoprotein / Golgi apparatus / Membrane / Signal-anchor / Transmembrane / Periplasm / Sugar transport
Function / homology
Function and homology information


heparan sulfate 2-O-sulfotransferase activity / HS-GAG biosynthesis / Transferases; Transferring sulfur-containing groups; Sulfotransferases / ureteric bud formation / heparan sulfate proteoglycan biosynthetic process, enzymatic modification / heparan sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process / heparin metabolic process / detection of maltose stimulus / maltose binding / maltose transport complex ...heparan sulfate 2-O-sulfotransferase activity / HS-GAG biosynthesis / Transferases; Transferring sulfur-containing groups; Sulfotransferases / ureteric bud formation / heparan sulfate proteoglycan biosynthetic process, enzymatic modification / heparan sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process / heparin metabolic process / detection of maltose stimulus / maltose binding / maltose transport complex / maltose transport / maltodextrin transmembrane transport / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / carbohydrate transport / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / gene expression / outer membrane-bounded periplasmic space / periplasmic space / Golgi membrane / DNA damage response / membrane / identical protein binding
Similarity search - Function
Heparan sulphate 2-O-sulfotransferase / Sulfotransferase / Sulfotransferase family / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase ...Heparan sulphate 2-O-sulfotransferase / Sulfotransferase / Sulfotransferase family / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
alpha-maltose / ADENOSINE-3'-5'-DIPHOSPHATE / Maltose/maltodextrin-binding periplasmic protein / Heparan sulfate 2-O-sulfotransferase 1
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
Gallus gallus (chicken)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsBethea, H.N. / Xu, D. / Liu, J. / Pedersen, L.C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2008
Title: Redirecting the substrate specificity of heparan sulfate 2-O-sulfotransferase by structurally guided mutagenesis.
Authors: Bethea, H.N. / Xu, D. / Liu, J. / Pedersen, L.C.
History
DepositionNov 3, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 23, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / 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_struct_assembly_gen / struct_asym / struct_conn / struct_ref_seq_dif / 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_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 20, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 2.2Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Maltose-binding periplasmic protein, Heparan sulfate 2-O-sulfotransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,0563
Polymers74,2861
Non-polymers7692
Water3,009167
1
A: Maltose-binding periplasmic protein, Heparan sulfate 2-O-sulfotransferase 1
hetero molecules

A: Maltose-binding periplasmic protein, Heparan sulfate 2-O-sulfotransferase 1
hetero molecules

A: Maltose-binding periplasmic protein, Heparan sulfate 2-O-sulfotransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)225,1689
Polymers222,8593
Non-polymers2,3086
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area17500 Å2
ΔGint-43 kcal/mol
Surface area72060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)152.647, 152.647, 85.686
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein Maltose-binding periplasmic protein, Heparan sulfate 2-O-sulfotransferase 1 / MMBP / Maltodextrin-binding protein / cHS2ST


Mass: 74286.336 Da / Num. of mol.: 1 / Fragment: P0AEX9 residues 27-392, Q76KB1 residues 69-356 / Mutation: E359A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria), (gene. exp.) Gallus gallus (chicken)
Gene: b4034, HS2ST, HS2ST1, JW3994, malE, HS2ST, HS2ST1, malE
Plasmid: modified pMAL-c2x / Production host: Escherichia coli (E. coli) / Strain (production host): OrigamiB(DE3)
References: UniProt: P0AEX9, UniProt: Q76KB1, Transferases; Transferring sulfur-containing groups; Sulfotransferases
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-A3P / ADENOSINE-3'-5'-DIPHOSPHATE / Adenosine 3',5'-bisphosphate


Type: RNA linking / Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 167 / 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: 3.88 Å3/Da / Density % sol: 68.29 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6
Details: Ammonium Citrate, Bis-tris-propane, Phenol, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 92 / Detector: CCD / Date: Oct 1, 2008 / Details: Varimax HF
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.65→50 Å / Num. all: 33196 / Num. obs: 33063 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.3 % / Biso Wilson estimate: 38.8 Å2 / Rsym value: 0.086 / Net I/σ(I): 14.1
Reflection shellResolution: 2.65→2.74 Å / Redundancy: 5.7 % / Mean I/σ(I) obs: 3.6 / Num. unique all: 3261 / Rsym value: 0.541 / % possible all: 99.3

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Processing

Software
NameVersionClassification
StructureStudiodata collection
MOLREPphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3DM0

3dm0


Resolution: 2.65→28.85 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 625197.83 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.243 1388 4.8 %RANDOM
Rwork0.2 ---
all0.2 33060 --
obs0.2 28726 86.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 27.9365 Å2 / ksol: 0.311599 e/Å3
Displacement parametersBiso mean: 46.1 Å2
Baniso -1Baniso -2Baniso -3
1-3.7 Å214.22 Å20 Å2
2--3.7 Å20 Å2
3----7.4 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.45 Å0.37 Å
Refinement stepCycle: LAST / Resolution: 2.65→28.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5186 0 50 167 5403
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d21.9
X-RAY DIFFRACTIONc_improper_angle_d0.87
X-RAY DIFFRACTIONc_mcbond_it1.261.5
X-RAY DIFFRACTIONc_mcangle_it2.152
X-RAY DIFFRACTIONc_scbond_it2.112
X-RAY DIFFRACTIONc_scangle_it3.062.5
LS refinement shellResolution: 2.65→2.82 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.329 208 5.2 %
Rwork0.297 3824 -
obs--73.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3carbohydrate.paramcarbohydrate.top
X-RAY DIFFRACTION4a3p.para3p.top
X-RAY DIFFRACTION5ion.paramion.top

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