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- PDB-6xkg: Crystal structure of 3-O-Sulfotransferase isoform 3 in complex wi... -

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Basic information

Entry
Database: PDB / ID: 6xkg
TitleCrystal structure of 3-O-Sulfotransferase isoform 3 in complex with 8mer oligosaccharide with 6S sulfation
ComponentsHeparan sulfate glucosamine 3-O-sulfotransferase 3A1
KeywordsTRANSFERASE / sulfotransferase / enzyme / PAPS / Heparan sulfate
Function / homology
Function and homology information


[heparan sulfate]-glucosamine 3-sulfotransferase 3 / [heparan sulfate]-glucosamine 3-sulfotransferase activity / glycosaminoglycan biosynthetic process / HS-GAG biosynthesis / sulfotransferase activity / heparan sulfate proteoglycan biosynthetic process / branching involved in ureteric bud morphogenesis / Golgi membrane / membrane
Similarity search - Function
Heparan sulfate sulfotransferase / Sulfotransferase domain / Sulfotransferase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-3'-5'-DIPHOSPHATE / P-NITROPHENOL / Heparan sulfate glucosamine 3-O-sulfotransferase 3A1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsPedersen, L.C. / Liu, J. / Wander, R.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)ZIA ES102645 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)HL094463 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)HL144970 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM128484 United States
CitationJournal: Rsc Chem Biol / Year: 2021
Title: Deciphering the substrate recognition mechanisms of the heparan sulfate 3- O -sulfotransferase-3.
Authors: Wander, R. / Kaminski, A.M. / Xu, Y. / Pagadala, V. / Krahn, J.M. / Pham, T.Q. / Liu, J. / Pedersen, L.C.
History
DepositionJun 26, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 23, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 15, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Heparan sulfate glucosamine 3-O-sulfotransferase 3A1
A: Heparan sulfate glucosamine 3-O-sulfotransferase 3A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,84517
Polymers62,4322
Non-polymers5,41315
Water12,376687
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B: Heparan sulfate glucosamine 3-O-sulfotransferase 3A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,24510
Polymers31,2161
Non-polymers3,0299
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Heparan sulfate glucosamine 3-O-sulfotransferase 3A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6007
Polymers31,2161
Non-polymers2,3846
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)133.760, 65.012, 92.235
Angle α, β, γ (deg.)90.000, 124.735, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11B-778-

HOH

21B-857-

HOH

DetailsThe biological assembly is unknown. Biophysical analysis is inconclusive but seems to indicate a monomer. In three different crystal forms, the same dimer is observed in the asymmetric unit.

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Components

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Protein , 1 types, 2 molecules BA

#1: Protein Heparan sulfate glucosamine 3-O-sulfotransferase 3A1 / Heparan sulfate D-glucosaminyl 3-O-sulfotransferase 3A1 / h3-OST-3A


Mass: 31215.963 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HS3ST3A1, 3OST3A1, HS3ST3A, UNQ2551/PRO6180 / Plasmid: pGEX4T3 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): -RIL
References: UniProt: Q9Y663, [heparan sulfate]-glucosamine 3-sulfotransferase 3

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Sugars , 2 types, 2 molecules

#2: Polysaccharide 2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid- ...2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid


Type: oligosaccharide / Mass: 1670.363 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
WURCS=2.0/3,6,5/[a2122A-1b_1-5][a2122h-1a_1-5_2*NSO/3=O/3=O_6*OSO/3=O/3=O][a2121A-1a_1-5_2*OSO/3=O/3=O]/1-2-3-2-3-2/a4-b1_b4-c1_c4-d1_d4-e1_e4-f1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpA]{[(4+1)][a-D-GlcpNSO36SO3]{[(4+1)][a-L-IdopA2SO3]{[(4+1)][a-D-GlcpNSO36SO3]{[(4+1)][a-L-IdopA2SO3]{[(4+1)][a-D-GlcpNSO36SO3]{}}}}}}LINUCSPDB-CARE
#3: Polysaccharide 2-acetamido-2-deoxy-6-O-sulfo-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-4)-2- ...2-acetamido-2-deoxy-6-O-sulfo-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid


Type: oligosaccharide / Mass: 2129.743 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
WURCS=2.0/4,8,7/[a2122A-1b_1-5][a2122h-1a_1-5_2*NSO/3=O/3=O_6*OSO/3=O/3=O][a2121A-1a_1-5_2*OSO/3=O/3=O][a2122h-1a_1-5_2*NCC/3=O_6*OSO/3=O/3=O]/1-2-3-2-3-2-1-4/a4-b1_b4-c1_c4-d1_d4-e1_e4-f1_f4-g1_g4-h1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpA]{[(4+1)][a-D-GlcpNSO36SO3]{[(4+1)][a-L-IdopA2SO3]{[(4+1)][a-D-GlcpNSO36SO3]{[(4+1)][a-L-IdopA2SO3]{[(4+1)][a-D-GlcpNSO36SO3]{[(4+1)][b-D-GlcpA]{[(4+1)][a-D-GlcpNAc6SO3]{}}}}}}}}LINUCSPDB-CARE

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Non-polymers , 5 types, 700 molecules

#4: Chemical ChemComp-NPO / P-NITROPHENOL


Mass: 139.109 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5NO3
#5: Chemical ChemComp-A3P / ADENOSINE-3'-5'-DIPHOSPHATE


Type: RNA linking / Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#7: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 687 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.64 Å3/Da / Density % sol: 53.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Protein: 15.5mg/ml 3ost3a, 4mM PAP, 5mM 8mer Nac/NS2S6S, 25mM Tris pH 7.5, 125mM NaCl, Reservoir: 0.1M Bicine and 10% MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.514 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Mar 5, 2019 / Details: varimaxHF
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.514 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. obs: 91530 / % possible obs: 97 % / Redundancy: 2.5 % / Biso Wilson estimate: 18.29 Å2 / Rmerge(I) obs: 0.045 / Rpim(I) all: 0.027 / Rrim(I) all: 0.053 / Net I/σ(I): 18.2
Reflection shellResolution: 1.55→1.58 Å / Rmerge(I) obs: 0.426 / Mean I/σ(I) obs: 1.98 / Num. unique obs: 4216 / CC1/2: 0.748 / Rpim(I) all: 0.396 / Rrim(I) all: 0.583 / % possible all: 90.2

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1T8U

1t8u


Resolution: 1.55→32.86 Å / SU ML: 0.148 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.5149
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.1826 2000 2.19 %random selection
Rwork0.1638 89491 --
obs0.1642 91491 96.51 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.9 Å2
Refinement stepCycle: LAST / Resolution: 1.55→32.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4184 0 334 687 5205
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01044764
X-RAY DIFFRACTIONf_angle_d1.06996491
X-RAY DIFFRACTIONf_chiral_restr0.0558732
X-RAY DIFFRACTIONf_plane_restr0.0073791
X-RAY DIFFRACTIONf_dihedral_angle_d14.941780
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.590.24761230.22675541X-RAY DIFFRACTION84.35
1.59-1.630.2141370.20886070X-RAY DIFFRACTION92.17
1.63-1.680.22231380.21116210X-RAY DIFFRACTION94.11
1.68-1.730.25871400.19646298X-RAY DIFFRACTION95.63
1.73-1.790.20211430.18966385X-RAY DIFFRACTION96.77
1.79-1.860.22791450.18376457X-RAY DIFFRACTION97.82
1.86-1.950.18631450.17566489X-RAY DIFFRACTION98.24
1.95-2.050.21141450.17786480X-RAY DIFFRACTION98.25
2.05-2.180.20241450.15926514X-RAY DIFFRACTION98.45
2.18-2.350.19561460.16416518X-RAY DIFFRACTION98.41
2.35-2.590.20411460.16766563X-RAY DIFFRACTION98.88
2.59-2.960.17581480.16616605X-RAY DIFFRACTION98.99
2.96-3.730.16851480.14886589X-RAY DIFFRACTION99.18
3.73-32.860.14451510.14436772X-RAY DIFFRACTION99.7
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.248058759957-0.119178493171-0.09092351581270.1460274291280.1049309093640.128914384203-0.0233502770824-0.0909818724859-0.05836506307670.04960893252210.0230849891193-0.02959991884270.0561270163566-0.0475761619512.88248815052E-80.151293806764-0.00203993172064-0.0003503189134410.135235751282-0.007326737211320.1306896672523.095747346-51.728712852363.4882041745
20.0911301955687-0.103747179897-0.05344172861520.1050572002530.01325612825530.0645445749443-0.1437085778350.0665904922653-0.3146428637640.07956529979950.03455871301370.04016026792470.257073255318-0.163535157568-0.00363275841540.192681350829-0.03318051733260.03208374709950.174920304672-0.01505826019940.165526940079.56194506659-57.738555915861.2524452544
30.6504427916140.0879979958486-0.03815426821090.4223281839610.01782569228020.327819250514-0.006015604349380.0495413255081-0.06214667113770.0101640792762-0.0005160797686750.001803345153660.0220502557651-0.168856262750.001885470012540.133420995156-0.003417095551830.01022550797730.144959646035-0.01992394967890.12078984807515.2118399133-51.130148656753.0442139785
40.6071865812390.0335143391076-0.5223458033160.579961526895-0.1802293141250.5009569608490.1136313181480.563573732312-0.361508094456-0.4869037034430.1600260755310.1124402931880.504100424054-0.2191796126140.2579369406980.289941697846-0.0352519561519-0.0627205774430.331886300806-0.1462799183790.29769396379712.3693729824-62.027977593929.8520786686
50.2438597409650.114663360339-0.1301650917910.1775327660710.01368075266770.0955206839061-0.09141868997890.168377434381-0.0598063375373-0.09436488286580.0416766729240.168030076219-0.0224513017373-0.1812669045520.0008283295716910.1635294426740.0210070208718-0.001819602321270.211372760821-0.002045063495380.1569521332097.8339686165-45.397099481344.8522629707
60.7938670574110.0473465942206-0.02775586207580.06444428983460.1198223124780.421530338481-0.004385110533340.119970048135-0.00125961820082-0.02752759280370.00526729655519-0.0374485208377-0.027740681090.0776684794914-0.000651803094540.147148381897-0.0005911998058290.01290466911810.133664993587-0.01406181857930.13983633553729.9759300188-48.171968337650.8847310285
70.332142937880.01334128706930.02897286219550.1424468049220.006220516967030.0551186640102-0.0001668344342520.4597654698380.113317533959-0.2663843100920.0266834081523-0.080074476248-0.297087311482-0.00349969530691-0.03212393911280.20854096879-0.009293487539550.01861424024050.283128054754-0.00162863687230.13095752515417.1348913232-43.322601786532.5660971775
80.2972132252630.106807982597-0.1840860244440.332202617218-0.1023032697710.081616654213-0.0439043870794-0.0309756043652-0.00619393473666-0.02378907922380.038112024394-0.09985323820340.00920599592470.01559215439016.40224552229E-80.141843115890.0179600828824-0.00229049632860.139270302405-0.00680715933580.17761281983753.0068484838-55.834142036968.7047380628
90.02991333513330.0111232890106-0.06494368188770.429663478158-0.07328318092670.106541240194-0.0867509588047-0.1872690737740.1117547216270.1037919032440.0914546137456-0.331651617196-0.05678653588860.237249624965-0.01682647979590.1584025127480.0101256379188-0.01505175738910.23659595573-0.0397028501680.25736843210761.401941017-49.751494704675.3114738316
100.163440490224-0.01461716235240.07336812737070.1467303203690.03379083116170.06356971210690.164590343001-0.450467431875-0.09972542157020.579731107314-0.114985906623-0.3970217434860.120441503948-0.05257629162720.03731005987940.388908911520.0076937837382-0.1289103349060.3049632033410.005069491232890.24197209571255.6451042835-51.840027129797.0924608276
110.0565075848747-0.0356005032447-0.02285698898970.2088314283430.02339596093750.0952099491263-0.192960490387-0.107482433159-0.01034815810.2420906484850.0739650358934-0.306081136314-0.1916572030550.18417397326-0.02100517418220.156409331985-0.0205657942997-0.06531705169180.233569321426-0.05698777728930.36332884519566.4750338137-43.712646881878.5170359537
120.644961120297-0.2312758512370.1855588628730.4453714091370.1804546729580.200109708389-0.0477360154443-0.1269292426940.1125978052060.087504747530.01762635857180.0221045891639-0.0874646318133-0.06723376342380.000538651543130.1528972059460.0106168997475-0.009029322603540.156039092324-0.0331953784840.15417160899841.6159164357-45.009748804977.1738654017
130.1211527065020.01038252782430.09787985809530.05029462890230.0044512479720.0775250939104-0.176770801019-0.2268580150070.2504364408810.304335825204-0.0212732654182-0.222301699164-0.278785032693-0.0658978631366-0.08862646591180.3235802172970.0535985387276-0.1256100908990.239557270806-0.09467576606010.28756359352156.9824519814-36.400187270692.1187883846
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'B' and (resid 141 through 180 )BA141 - 1801 - 40
22chain 'B' and (resid 181 through 202 )BA181 - 20241 - 62
33chain 'B' and (resid 203 through 259 )BA203 - 25963 - 119
44chain 'B' and (resid 260 through 283 )BA260 - 283120 - 143
55chain 'B' and (resid 284 through 303 )BA284 - 303144 - 163
66chain 'B' and (resid 304 through 376 )BA304 - 376164 - 236
77chain 'B' and (resid 377 through 406 )BA377 - 406237 - 266
88chain 'A' and (resid 147 through 215 )AB147 - 2151 - 69
99chain 'A' and (resid 216 through 244 )AB216 - 24470 - 98
1010chain 'A' and (resid 245 through 290 )AB245 - 29099 - 141
1111chain 'A' and (resid 291 through 303 )AB291 - 303142 - 154
1212chain 'A' and (resid 304 through 376 )AB304 - 376155 - 227
1313chain 'A' and (resid 377 through 406 )AB377 - 406228 - 257

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