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- PDB-5t03: Crystal structure of heparan sulfate 6-O-sulfotransferase with bo... -

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Basic information

Entry
Database: PDB / ID: 5t03
TitleCrystal structure of heparan sulfate 6-O-sulfotransferase with bound PAP and glucuronic acid containing hexasaccharide substrate
Componentsmaltose binding protein - heparan sulfate 6-O-sulfotransferase isoform 3 fusion protein
KeywordsTRANSFERASE / heparan sulfate / sulfotransferase / complex
Function / homology
Function and homology information


heparan sulfate 6-O-sulfotransferase activity / HS-GAG biosynthesis / Transferases; Transferring sulfur-containing groups; Sulfotransferases / heparan sulfate proteoglycan biosynthetic process, enzymatic modification / 3'-phosphoadenosine 5'-phosphosulfate binding / sulfotransferase activity / oligosaccharide binding / detection of maltose stimulus / maltose binding / maltose transport complex ...heparan sulfate 6-O-sulfotransferase activity / HS-GAG biosynthesis / Transferases; Transferring sulfur-containing groups; Sulfotransferases / heparan sulfate proteoglycan biosynthetic process, enzymatic modification / 3'-phosphoadenosine 5'-phosphosulfate binding / sulfotransferase activity / oligosaccharide binding / 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 / outer membrane-bounded periplasmic space / periplasmic space / DNA damage response / membrane
Similarity search - Function
Heparan sulphate 6-sulfotransferase/Protein-tyrosine 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 nucleoside triphosphate hydrolase
Similarity search - Domain/homology
alpha-maltotetraose / ADENOSINE-3'-5'-DIPHOSPHATE / P-NITROPHENOL / L(+)-TARTARIC ACID / Heparan-sulfate 6-O-sulfotransferase 3-B / Maltose/maltodextrin-binding periplasmic protein / Maltose/maltodextrin-binding periplasmic protein
Similarity search - Component
Biological speciesEscherichia coli O157:H7 (bacteria)
Danio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsPedersen, L.C. / Moon, A.F. / Krahn, J.M. / Liu, J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM102137 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)HL094463 United States
CitationJournal: ACS Chem. Biol. / Year: 2017
Title: Structure Based Substrate Specificity Analysis of Heparan Sulfate 6-O-Sulfotransferases.
Authors: Xu, Y. / Moon, A.F. / Xu, S. / Krahn, J.M. / Liu, J. / Pedersen, L.C.
History
DepositionAug 15, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 1, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Data collection / Category: chem_comp / pdbx_audit_support
Item: _chem_comp.type / _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / 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 / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / 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_alt_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_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: maltose binding protein - heparan sulfate 6-O-sulfotransferase isoform 3 fusion protein
B: maltose binding protein - heparan sulfate 6-O-sulfotransferase isoform 3 fusion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,02941
Polymers157,1142
Non-polymers6,91539
Water16,484915
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A: maltose binding protein - heparan sulfate 6-O-sulfotransferase isoform 3 fusion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,24125
Polymers78,5571
Non-polymers3,68424
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: maltose binding protein - heparan sulfate 6-O-sulfotransferase isoform 3 fusion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,78816
Polymers78,5571
Non-polymers3,23015
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)75.778, 128.396, 179.722
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein maltose binding protein - heparan sulfate 6-O-sulfotransferase isoform 3 fusion protein / MBP / MMBP / Maltodextrin-binding protein / HS 6-OST-3


Mass: 78557.203 Da / Num. of mol.: 2
Mutation: D82A, K83A, E172A, N173A, K239A, E359A, K362A, D363A
Source method: isolated from a genetically manipulated source
Details: This is an N-terminal MBP fusion to HS 6-O-sulfotransferase from zebrafish isoform 3. To keep the correct numbering with the 6-O-sulfotransferase add 1000.
Source: (gene. exp.) Escherichia coli O157:H7 (bacteria), (gene. exp.) Danio rerio (zebrafish)
Gene: malE, Z5632, ECs5017, hs6st3 / Production host: Escherichia coli (E. coli)
References: UniProt: P0AEY0, UniProt: A0MGZ7, UniProt: P0AEX9*PLUS, Transferases; Transferring sulfur-containing groups; Sulfotransferases

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Sugars , 2 types, 4 molecules

#2: Polysaccharide 2-deoxy-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-4)-2-deoxy-2- ...2-deoxy-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-4)-2-deoxy-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-4)-2-deoxy-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid


Type: oligosaccharide / Mass: 1270.043 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNSa1-4DGlcpAb1-4DGlcpNSa1-4DGlcpAb1-4DGlcpNSa1-4DGlcpAb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,6,5/[a2122A-1b_1-5][a2122h-1a_1-5_2*NSO/3=O/3=O]/1-2-1-2-1-2/a4-b1_b4-c1_c4-d1_d4-e1_e4-f1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpA]{[(4+1)][a-D-GlcpNSO3]{[(4+1)][b-D-GlcpA]{[(4+1)][a-D-GlcpNSO3]{[(4+1)][b-D-GlcpA]{[(4+1)][a-D-GlcpNSO3]{}}}}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltotetraose


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 666.578 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltotetraose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,4,3/[a2122h-1a_1-5]/1-1-1-1/a4-b1_b4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}}}LINUCSPDB-CARE

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Non-polymers , 7 types, 950 molecules

#4: Chemical ChemComp-A3P / ADENOSINE-3'-5'-DIPHOSPHATE / Adenosine 3',5'-bisphosphate


Type: RNA linking / Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2
#5: Chemical ChemComp-NPO / P-NITROPHENOL / 4-Nitrophenol


Mass: 139.109 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H5NO3
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 16
Source method: isolated from a genetically manipulated source
Formula: C2H6O2
#7: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Formula: Cl
#8: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#9: Chemical
ChemComp-TLA / L(+)-TARTARIC ACID / Tartaric acid


Mass: 150.087 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H6O6
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 915 / 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: 2.78 Å3/Da / Density % sol: 55.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100mM Tris pH 7.5, 200mM di-sodium tartrate, 18-19% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Mar 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 102512 / % possible obs: 99.7 % / Redundancy: 6 % / Net I/σ(I): 6.3

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→38.648 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 20.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2117 2273 2.22 %
Rwork0.1735 --
obs0.1744 102388 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→38.648 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10463 0 441 915 11819
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00611256
X-RAY DIFFRACTIONf_angle_d0.78715333
X-RAY DIFFRACTIONf_dihedral_angle_d11.5226560
X-RAY DIFFRACTIONf_chiral_restr0.0491718
X-RAY DIFFRACTIONf_plane_restr0.0051938
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1001-2.14580.2681340.21025866X-RAY DIFFRACTION95
2.1458-2.19570.26571390.19426153X-RAY DIFFRACTION99
2.1957-2.25060.22651420.19016165X-RAY DIFFRACTION99
2.2506-2.31150.24481400.18856215X-RAY DIFFRACTION100
2.3115-2.37950.22611390.18746211X-RAY DIFFRACTION100
2.3795-2.45620.25831440.18786246X-RAY DIFFRACTION100
2.4562-2.5440.23891400.18696219X-RAY DIFFRACTION100
2.544-2.64590.25361420.18116242X-RAY DIFFRACTION100
2.6459-2.76620.23031380.18656269X-RAY DIFFRACTION100
2.7662-2.9120.24661460.1916296X-RAY DIFFRACTION100
2.912-3.09440.25811420.19326222X-RAY DIFFRACTION100
3.0944-3.33320.21391440.18446309X-RAY DIFFRACTION100
3.3332-3.66840.20321440.16856336X-RAY DIFFRACTION100
3.6684-4.19870.16441440.14696334X-RAY DIFFRACTION100
4.1987-5.28780.18531460.1466404X-RAY DIFFRACTION100
5.2878-38.65430.18271490.17496628X-RAY DIFFRACTION100
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)
10.2867-0.3896-0.28570.48360.22720.5970.0360.3315-0.0601-0.1775-0.08220.3622-0.1283-0.174400.32430.0071-0.0030.3093-0.04330.38169.4067-23.9993-26.5891
20.2977-0.08240.07430.12660.16590.2581-0.153-0.2-0.09970.46360.13250.43430.0139-0.0638-0.03160.45760.04290.16830.31750.02050.37586.1563-20.9122-9.8344
30.38080.38330.24760.91850.0520.47990.0431-0.0695-0.020.2190.0215-0.15490.10780.1074-00.32040.0583-0.02860.2542-0.02260.201536.2301-18.3445-12.7753
41.0328-0.09690.11311.15550.24490.6619-0.0666-0.005-0.07740.24130.05950.09410.14410.0858-00.32010.03920.02690.18690.0090.188725.7403-23.493-15.6165
50.00690.0004-0.00360.0150.01010.02850.0961-0.3176-0.15970.25270.14850.1326-0.1033-0.11300.5190.04510.01510.35210.03090.266727.69-23.6948-3.9002
60.3025-0.2510.04140.19010.00360.0813-0.06930.04240.21420.16640.0233-0.06840.00260.0698-00.3191-0.00180.00440.261-0.00540.351324.27942.6257-16.3929
70.69-0.24260.17450.40830.19720.75910.07330.19950.3267-0.1116-0.0671-0.0885-0.3746-0.15640.00380.26390.06670.0580.20540.06790.27191.305330.1448-32.3827
81.5483-0.1977-0.07320.78350.06050.52090.05050.3656-0.1703-0.05910.009-0.0277-0.0258-0.08430.05870.12570.01990.02090.2496-0.01190.1714.1959.3039-37.3384
90.85810.08070.20110.18220.12610.71850.0609-0.1405-0.11170.17610.0037-0.05530.0024-0.16400.20960.03270.02290.22930.02910.23581.30815.8372-19.7167
100.497-0.33520.07640.4198-0.43840.41870.023-0.0831-0.11330.35020.0463-0.07-0.0029-0.00430.00390.19430.0109-0.00240.18570.03010.166112.456219.4268-13.5234
111.1470.26690.40070.26580.02670.7720.38370.0642-0.35590.2464-0.0754-0.36540.56660.23830.13340.5761-0.0316-0.2140.2944-0.01460.410324.280610.63315.1349
121.0797-0.2030.16990.98230.13890.66170.383-0.2928-0.25410.3875-0.19250.15750.589-0.71960.31660.5972-0.3365-0.06480.59550.07320.2515-3.54658.69739.9761
130.6819-0.30120.31920.88310.56371.08510.20640.1380.12350.1551-0.0932-0.27320.27990.00320.02630.4597-0.0878-0.080.33810.03980.300617.253517.458912.3061
140.54340.03030.02470.14220.17260.42990.2846-0.1905-0.18370.2559-0.2437-0.21210.322-0.20390.00560.6921-0.2283-0.13780.45120.09370.38645.333310.47916.9449
150.1075-0.19150.07850.65590.26290.6907-0.30830.46830.1546-0.65170.4183-0.445-0.35080.41650.12070.5451-0.1629-0.01420.42360.04870.44317.4884-10.869831.4918
160.4820.0306-0.14470.5838-0.14350.6544-0.0142-0.0384-0.13220.00540.0103-0.04580.2423-0.0502-00.216-0.0128-0.010.16150.02490.2488-1.8661-30.907248.8444
170.99130.27920.23480.75210.08090.48830.0064-0.05340.05030.09190.0058-0.01040.0579-0.0303-00.1105-0.0001-0.00630.15330.01730.1488-1.4147-10.892257.3136
180.28280.1411-0.21430.24840.27430.4903-0.05940.20790.1283-0.08210.0857-0.0627-0.0609-0.0715-00.1724-0.0208-0.02320.2280.01410.221-3.5052-15.920938.1908
190.52920.25190.04990.371-0.31480.5882-0.12940.1550.0397-0.12890.05390.0143-0.0802-0.0352-0.08220.1617-0.05570.01110.23050.01450.2136.1111-12.1237.1072
200.027-0.01980.00430.00150.0026-0.00740.69520.3015-0.03960.1775-0.05280.00730.17560.62800.7271-0.11750.1570.8029-0.19780.718317.6864-29.0618.1492
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 2:66)
2X-RAY DIFFRACTION2(chain A and resid 67:107)
3X-RAY DIFFRACTION3(chain A and resid 108:175)
4X-RAY DIFFRACTION4(chain A and resid 176:320)
5X-RAY DIFFRACTION5(chain A and resid 321:327)
6X-RAY DIFFRACTION6(chain A and resid 328:1087)
7X-RAY DIFFRACTION7(chain A and resid 1088:1169)
8X-RAY DIFFRACTION8(chain A and resid 1170:1291)
9X-RAY DIFFRACTION9(chain A and resid 1292:1345)
10X-RAY DIFFRACTION10(chain A and resid 1346:1383)
11X-RAY DIFFRACTION11(chain B and resid 2:111)
12X-RAY DIFFRACTION12(chain B and resid 112:243)
13X-RAY DIFFRACTION13(chain B and resid 244:307)
14X-RAY DIFFRACTION14(chain B and resid 308:355)
15X-RAY DIFFRACTION15(chain B and resid 356:1086)
16X-RAY DIFFRACTION16(chain B and resid 1087:1170)
17X-RAY DIFFRACTION17(chain B and resid 1171:1290)
18X-RAY DIFFRACTION18(chain B and resid 1291:1344)
19X-RAY DIFFRACTION19(chain B and resid 1345:1373)
20X-RAY DIFFRACTION20(chain B and resid 1374:1390)

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  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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