[English] 日本語
Yorodumi
- PDB-5t0a: Crystal Structure of Heparan Sulfate 6-O-Sulfotransferase with bo... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5t0a
TitleCrystal Structure of Heparan Sulfate 6-O-Sulfotransferase with bound PAP and heptasaccharide 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 / Resolution: 1.95 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: Advisory / Atomic model ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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 / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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)164,08237
Polymers157,1142
Non-polymers6,96835
Water18,2131011
1
A: maltose binding protein - heparan sulfate 6-O-sulfotransferase isoform 3 fusion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,28624
Polymers78,5571
Non-polymers3,72923
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)81,79613
Polymers78,5571
Non-polymers3,23912
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)75.775, 128.291, 178.929
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
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 the zebrafish 6-O-sulfotransferase isoform 3. To get the correct numbering for the 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

-
Sugars , 3 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)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid


Type: oligosaccharide / Mass: 1350.107 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/3,6,5/[a2122A-1b_1-5][a2122h-1a_1-5_2*NSO/3=O/3=O][a2121A-1a_1-5_2*OSO/3=O/3=O]/1-2-3-2-1-2/a4-b1_b4-c1_c4-d1_d4-e1_e4-f1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpA]{[(4+1)][a-D-GlcpNSO3]{[(4+1)][a-L-IdopA2SO3]{[(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
#4: Polysaccharide beta-D-glucopyranuronic acid-(1-4)-2-deoxy-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-beta-D- ...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)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid


Type: oligosaccharide / Mass: 1526.231 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/3,7,6/[a2122A-1b_1-5][a2122h-1a_1-5_2*NSO/3=O/3=O][a2121A-1a_1-5_2*OSO/3=O/3=O]/1-2-3-2-1-2-1/a4-b1_b4-c1_c4-d1_d4-e1_e4-f1_f4-g1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpA]{[(4+1)][a-D-GlcpNSO3]{[(4+1)][a-L-IdopA2SO3]{[(4+1)][a-D-GlcpNSO3]{[(4+1)][b-D-GlcpA]{[(4+1)][a-D-GlcpNSO3]{[(4+1)][b-D-GlcpA]{}}}}}}}LINUCSPDB-CARE

-
Non-polymers , 7 types, 1042 molecules

#5: Chemical ChemComp-NPO / P-NITROPHENOL / 4-Nitrophenol


Mass: 139.109 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5NO3
#6: 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
#7: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C2H6O2
#8: Chemical ChemComp-TLA / L(+)-TARTARIC ACID / Tartaric acid


Mass: 150.087 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H6O6
#9: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#10: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#11: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1011 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.77 Å3/Da / Density % sol: 55.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 25mM Tris pH 7.5 200mM disodium tartrate 18-19% PEG3350 1mM PAP 10mM oligosaccharide 5mM maltose

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Apr 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 126425 / % possible obs: 99.2 % / Redundancy: 6.5 % / Net I/σ(I): 8.2

-
Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 1.95→37.842 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.97
RfactorNum. reflection% reflection
Rfree0.2131 2803 2.22 %
Rwork0.1802 --
obs0.1809 126346 99.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.95→37.842 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10457 0 442 1011 11910
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00811254
X-RAY DIFFRACTIONf_angle_d1.15715319
X-RAY DIFFRACTIONf_dihedral_angle_d20.1014042
X-RAY DIFFRACTIONf_chiral_restr0.0661725
X-RAY DIFFRACTIONf_plane_restr0.0051936
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9497-1.98330.30141330.23365835X-RAY DIFFRACTION95
1.9833-2.01940.3041400.23246097X-RAY DIFFRACTION99
2.0194-2.05820.26621370.22136115X-RAY DIFFRACTION99
2.0582-2.10020.24961400.21366114X-RAY DIFFRACTION99
2.1002-2.14590.24261400.19966108X-RAY DIFFRACTION99
2.1459-2.19580.2391410.19396121X-RAY DIFFRACTION99
2.1958-2.25070.24381340.1946160X-RAY DIFFRACTION99
2.2507-2.31150.24021400.19366122X-RAY DIFFRACTION99
2.3115-2.37950.22211380.19266189X-RAY DIFFRACTION99
2.3795-2.45630.26131420.18996172X-RAY DIFFRACTION100
2.4563-2.54410.22621420.19046167X-RAY DIFFRACTION100
2.5441-2.64590.2531400.18876188X-RAY DIFFRACTION100
2.6459-2.76630.24091410.19456209X-RAY DIFFRACTION100
2.7663-2.91210.26051430.19576230X-RAY DIFFRACTION100
2.9121-3.09450.2621380.19296223X-RAY DIFFRACTION100
3.0945-3.33330.21791410.19116258X-RAY DIFFRACTION100
3.3333-3.66850.18831430.17196261X-RAY DIFFRACTION100
3.6685-4.19870.17031420.15146272X-RAY DIFFRACTION99
4.1987-5.28770.17191440.15036294X-RAY DIFFRACTION99
5.2877-37.84930.18711440.18066408X-RAY DIFFRACTION97

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • 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

-
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

Read more