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- PDB-1t8u: Crystal Structure of human 3-O-Sulfotransferase-3 with bound PAP ... -

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Basic information

Entry
Database: PDB / ID: 1t8u
TitleCrystal Structure of human 3-O-Sulfotransferase-3 with bound PAP and tetrasaccharide substrate
Componentsheparan sulfate D-glucosaminyl 3-O-sulfotransferase 3A1
KeywordsTRANSFERASE / alpha-beta motif / substrate-binding cleft
Function / homology
Function and homology information


[heparan sulfate]-glucosamine 3-sulfotransferase 3 / [heparan sulfate]-glucosamine 3-sulfotransferase 3 activity / [heparan sulfate]-glucosamine 3-sulfotransferase 1 activity / heparan sulfate proteoglycan biosynthetic process, enzymatic modification / HS-GAG biosynthesis / glycosaminoglycan biosynthetic process / sulfotransferase activity / branching involved in ureteric bud morphogenesis / Golgi membrane / membrane
Similarity search - Function
Heparan sulfate sulfotransferase / Sulfotransferase domain / Sulfotransferase domain / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-3'-5'-DIPHOSPHATE / : / Heparan sulfate glucosamine 3-O-sulfotransferase 3A1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsMoon, A.F. / Edavettal, S.C. / Krahn, J.M. / Munoz, E.M. / Negishi, M. / Linhardt, R.J. / Liu, J. / Pedersen, L.C.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Structural analysis of the sulfotransferase (3-o-sulfotransferase isoform 3) involved in the biosynthesis of an entry receptor for herpes simplex virus 1
Authors: Moon, A.F. / Edavettal, S.C. / Krahn, J.M. / Munoz, E.M. / Negishi, M. / Linhardt, R.J. / Liu, J. / Pedersen, L.C.
History
DepositionMay 13, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: 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 / 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_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / 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_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Apr 3, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 300BIOMOLECULE: THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). ...BIOMOLECULE: THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). THE BIOLOGICAL UNIT IS UNKNOWN.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: heparan sulfate D-glucosaminyl 3-O-sulfotransferase 3A1
B: heparan sulfate D-glucosaminyl 3-O-sulfotransferase 3A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,4098
Polymers62,2582
Non-polymers2,1516
Water6,449358
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7710 Å2
ΔGint-58 kcal/mol
Surface area22790 Å2
MethodPISA
2
A: heparan sulfate D-glucosaminyl 3-O-sulfotransferase 3A1
B: heparan sulfate D-glucosaminyl 3-O-sulfotransferase 3A1
hetero molecules

A: heparan sulfate D-glucosaminyl 3-O-sulfotransferase 3A1
B: heparan sulfate D-glucosaminyl 3-O-sulfotransferase 3A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,81816
Polymers124,5164
Non-polymers4,30312
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area18960 Å2
ΔGint-124 kcal/mol
Surface area42040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.806, 154.525, 91.931
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein / Sugars , 2 types, 3 molecules AB

#1: Protein heparan sulfate D-glucosaminyl 3-O-sulfotransferase 3A1 / HEPARIN-GLUCOSAMINE 3-O-SULFOTRANSFERASE / 3-OST-3


Mass: 31128.885 Da / Num. of mol.: 2 / Fragment: catalytic domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: h3-OST-3 / Plasmid: pGEX-4T3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus-RIL / References: GenBank: 5174465, UniProt: Q9Y663*PLUS
#2: Polysaccharide 4-deoxy-2-O-sulfo-alpha-L-threo-hex-4-enopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)- ...4-deoxy-2-O-sulfo-alpha-L-threo-hex-4-enopyranuronic 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


Type: oligosaccharide / Mass: 1154.940 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/3,4,3/[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][a21eEA-1a_1-5_2*OSO/3=O/3=O]/1-2-1-3/a4-b1_b4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[][a-D-GlcpNSO36SO3]{[(4+1)][a-L-IdopA2SO3]{[(4+1)][a-D-GlcpNSO36SO3]{[(4+1)][b-D-4-deoxy-GlcpA2SO3]{}}}}LINUCSPDB-CARE

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Non-polymers , 4 types, 363 molecules

#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 358 / 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: 2 Å3/Da / Density % sol: 38.5 %
Crystal growTemperature: 297 K / Method: micro-seeding / pH: 5.5
Details: sodium citrate, ammonium acetate, PEG 4000, PAP, pH 5.5, micro-seeding, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 17, 2004 / Details: Osmic mirrors
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 42327 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 15.5 Å2 / Rsym value: 0.054 / Net I/σ(I): 18.2
Reflection shellHighest resolution: 1.95 Å / Redundancy: 2.1 % / Num. unique all: 4178 / Rsym value: 0.024 / % possible all: 99.4

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Processing

Software
NameVersionClassification
CNS1refinement
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: h3-OST-3 with bound PAP

Resolution: 1.95→50 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 346751.18 / 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
Rfree0.222 2019 5 %RANDOM
Rwork0.199 ---
all0.2 40359 --
obs0.199 38340 95.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 52.9242 Å2 / ksol: 0.3827 e/Å3
Displacement parametersBiso mean: 28.5 Å2
Baniso -1Baniso -2Baniso -3
1--2.29 Å20 Å20 Å2
2---5.19 Å20 Å2
3---7.47 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 1.95→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4328 0 131 358 4817
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d21
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_mcbond_it1.311.5
X-RAY DIFFRACTIONc_mcangle_it2.012
X-RAY DIFFRACTIONc_scbond_it1.992
X-RAY DIFFRACTIONc_scangle_it2.942.5
LS refinement shellResolution: 1.95→2.07 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.276 307 5.1 %
Rwork0.252 5745 -
obs--86.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION13OST3.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.TOP
X-RAY DIFFRACTION3ION.TOP
X-RAY DIFFRACTION4PAP2_SO4.TOP
X-RAY DIFFRACTION5DNA-RNA.TOP

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