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- PDB-7sce: Ternary complex of fixed-arm Trx-3ost5 (I299E) with 8mer-2 octasa... -

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Basic information

Entry
Database: PDB / ID: 7sce
TitleTernary complex of fixed-arm Trx-3ost5 (I299E) with 8mer-2 octasaccharide substrate and co-factor product PAP
ComponentsThioredoxin 1,Heparan sulfate glucosamine 3-O-sulfotransferase 5
KeywordsTRANSFERASE/SUBSTRATE / sulfotransferase / heparan sulfate / oligosaccharide / complex / TRANSFERASE / TRANSFERASE-SUBSTRATE complex
Function / homology
Function and homology information


protein sulfation / [heparan sulfate]-glucosamine 3-sulfotransferase 1 / [heparan sulfate]-glucosamine 3-sulfotransferase 1 activity / heparan sulfate proteoglycan biosynthetic process, enzymatic modification / 3'-phosphoadenosine 5'-phosphosulfate binding / negative regulation of coagulation / HS-GAG biosynthesis / regulation of viral entry into host cell / DNA polymerase processivity factor activity / protein-disulfide reductase activity ...protein sulfation / [heparan sulfate]-glucosamine 3-sulfotransferase 1 / [heparan sulfate]-glucosamine 3-sulfotransferase 1 activity / heparan sulfate proteoglycan biosynthetic process, enzymatic modification / 3'-phosphoadenosine 5'-phosphosulfate binding / negative regulation of coagulation / HS-GAG biosynthesis / regulation of viral entry into host cell / DNA polymerase processivity factor activity / protein-disulfide reductase activity / cell redox homeostasis / Golgi membrane / membrane / cytoplasm / cytosol
Similarity search - Function
Heparan sulfate sulfotransferase / Sulfotransferase domain / Sulfotransferase domain / Thioredoxin / Thioredoxin / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Thioredoxin-like superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-3'-5'-DIPHOSPHATE / Thioredoxin 1 / Heparan sulfate glucosamine 3-O-sulfotransferase 5
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsWander, R. / Kaminski, A.M. / Krahn, J.M. / Liu, J. / Pedersen, L.C.
Funding support United States, 6items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)1ZIA-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
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM134738 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)HL139197 United States
CitationJournal: Acs Catalysis / Year: 2021
Title: Structural and Substrate Specificity Analysis of 3-O-Sulfotransferase Isoform 5 to Synthesize Heparan Sulfate
Authors: Wander, R. / Kaminski, A.M. / Wang, Z. / Stancanelli, E. / Xu, Y. / Pagadala, V. / Li, J. / Krahn, J.M. / Pham, T.Q. / Liu, J. / Pedersen, L.C.
History
DepositionSep 27, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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

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Assembly

Deposited unit
A: Thioredoxin 1,Heparan sulfate glucosamine 3-O-sulfotransferase 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8393
Polymers42,8211
Non-polymers2,0182
Water95553
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3210 Å2
ΔGint16 kcal/mol
Surface area17030 Å2
Unit cell
Length a, b, c (Å)54.421, 58.997, 151.045
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Thioredoxin 1,Heparan sulfate glucosamine 3-O-sulfotransferase 5 / Trx-1 / Heparan sulfate D-glucosaminyl 3-O-sulfotransferase 5 / 3-OST-5 / Heparan sulfate 3-O- ...Trx-1 / Heparan sulfate D-glucosaminyl 3-O-sulfotransferase 5 / 3-OST-5 / Heparan sulfate 3-O-sulfotransferase 5 / h3-OST-5


Mass: 42821.449 Da / Num. of mol.: 1 / Mutation: I299E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Homo sapiens (human)
Strain: K12
Gene: trxA, fipA, tsnC, b3781, JW5856, HS3ST5, 3OST5, HS3OST5
Plasmid: pET32bX / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 (DE3)
References: UniProt: P0AA25, UniProt: Q8IZT8, [heparan sulfate]-glucosamine 3-sulfotransferase 1
#2: Polysaccharide 2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-4)-2- ...2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-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


Type: oligosaccharide / Mass: 1590.299 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
WURCS=2.0/3,6,5/[a2121A-1a_1-5_2*OSO/3=O/3=O][a2122h-1a_1-5_2*NSO/3=O/3=O_6*OSO/3=O/3=O][a2122A-1b_1-5]/1-2-3-2-3-2/a4-b1_b4-c1_c4-d1_d4-e1_e4-f1WURCSPDB2Glycan 1.1.0
[][L-1,6-deoxy-Idop2SO3]{[(4+1)][a-D-2-deoxy-Glcp6SO3]{[(4+1)][b-D-GlcpA]{[(4+1)][a-D-2-deoxy-Glcp6SO3]{[(4+1)][b-D-GlcpA]{[(4+1)][a-D-2-deoxy-Glcp6SO3]{}}}}}}LINUCSPDB-CARE
#3: Chemical ChemComp-A3P / ADENOSINE-3'-5'-DIPHOSPHATE


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


Mass: 18.015 Da / Num. of mol.: 53 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.9 Å3/Da / Density % sol: 57.6 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 85mM sodium acetate pH 4.6, 0.17M ammonium acetate, 25.5% (w/v) PEG4000, 15% (v/v) ethylene glycol

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 10, 2021
RadiationMonochromator: DOUBLE CRYSTAL SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.75→50 Å / Num. obs: 13239 / % possible obs: 99.1 % / Redundancy: 4.9 % / Biso Wilson estimate: 31.65 Å2 / CC1/2: 0.992 / CC star: 0.998 / Rsym value: 0.163 / Net I/σ(I): 7.46
Reflection shellResolution: 2.75→2.8 Å / Mean I/σ(I) obs: 1.54 / Num. unique obs: 642 / CC1/2: 0.661 / CC star: 0.892 / Rsym value: 0.671

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BD9

3bd9


Resolution: 2.75→40 Å / SU ML: 0.3285 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.8839
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.246 661 5.01 %random
Rwork0.1879 12535 --
obs0.1907 13196 98.24 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.26 Å2
Refinement stepCycle: LAST / Resolution: 2.75→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2883 0 124 53 3060
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00363084
X-RAY DIFFRACTIONf_angle_d0.76054216
X-RAY DIFFRACTIONf_chiral_restr0.0497493
X-RAY DIFFRACTIONf_plane_restr0.0056516
X-RAY DIFFRACTIONf_dihedral_angle_d13.68271108
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.75-2.950.29861280.24422367X-RAY DIFFRACTION94.4
2.95-3.240.30391300.21762486X-RAY DIFFRACTION99.7
3.25-3.710.26111360.1922511X-RAY DIFFRACTION99.85
3.71-4.680.20211290.15582539X-RAY DIFFRACTION99.37
4.68-400.2211380.1782632X-RAY DIFFRACTION97.88
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)
10.03719840111240.0126736805926-0.02578196700860.01153079061-0.05765525584060.083696477980.153870528918-0.206108273025-0.1572255148880.130503419036-0.01115704412380.135537535324-0.362438461880.3408679159480.06254632350340.385635522019-0.1627287549990.09525938836350.4983643763130.39299343779-0.0796270952121-20.65287699058.72714198196-10.5010804948
20.0268541970705-0.02538166132450.0109831142490.0246416710206-0.01260346237930.0554243687567-0.002371398564540.005316109770120.00565362137604-0.0107513412054-0.01210776586480.00685310332605-0.00394692985502-0.002222622337860.0002908839271860.5147856154040.01214168059350.03360667942480.5036624610870.1756050785480.360602528795-21.553625952224.156946737-21.8480000587
30.381512190925-0.230280201276-0.07384713029190.324861661492-0.09669419022650.177210612862-0.0248124701562-0.00271105348455-0.0263598745047-0.06531668729080.02757917284520.004970713298320.0343423355291-0.0206840639143-0.01764244807650.0539816405953-0.01904275342410.009112142696540.03407596551660.003647065717790.0753048577855-8.6284520554911.1311223833-47.414673182
4-0.0100176965023-0.00395166331470.00474657550262-0.00262268809558-0.01600009783680.00355198967560.0364815552914-0.01134374346270.0773556894081-0.112119097356-0.01900728893730.0624056554178-0.0588108262862-0.0638366291281-4.57968445369E-70.6121405592730.0649450534472-0.1948778655060.5391722704070.05847866675950.62527585401-16.654035682117.1536641829-57.4559674026
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain A and resid 3:108AA3 - 1081 - 106
22chain A and resid 109:111AA109 - 111107 - 109
33chain A and resid 1086:1346AA1086 - 1346110 - 370
44chain C and resid 1:6CB1 - 6

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