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- PDB-5g2t: BT1596 in complex with its substrate 4,5 unsaturated uronic acid ... -

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Basic information

Entry
Database: PDB / ID: 5g2t
TitleBT1596 in complex with its substrate 4,5 unsaturated uronic acid alpha 1,4 D-Glucosamine-2-N, 6-O-disulfate
Components2-O GLYCOSAMINOGLYCAN SULFATASE
KeywordsHYDROLASE / GLYCOSAMINOGLYCAN SULFATASE
Function / homology
Function and homology information


glucuronate-2-sulfatase activity / Hydrolases; Acting on ester bonds; Sulfuric-ester hydrolases / arylsulfatase activity / metal ion binding
Similarity search - Function
: / N-sulphoglucosamine sulphohydrolase, C-terminal / Sulfatase, N-terminal / Sulfatase / Alkaline Phosphatase, subunit A / Alkaline Phosphatase, subunit A / Alkaline-phosphatase-like, core domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-UAP / Delta 4,5-hexuronate-2-O-sulfatase
Similarity search - Component
Biological speciesBACTEROIDES THETAIOTAOMICRON (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsCartmell, A. / Lowe, E.C. / Basle, A. / Crouch, L.I. / Czjzek, M. / Turnbull, J. / Henrissat, B. / Terrapon, N. / Thomas, S. / Murray, H. ...Cartmell, A. / Lowe, E.C. / Basle, A. / Crouch, L.I. / Czjzek, M. / Turnbull, J. / Henrissat, B. / Terrapon, N. / Thomas, S. / Murray, H. / Firbank, S.J. / Bolam, D.N.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: How members of the human gut microbiota overcome the sulfation problem posed by glycosaminoglycans.
Authors: Cartmell, A. / Lowe, E.C. / Basle, A. / Firbank, S.J. / Ndeh, D.A. / Murray, H. / Terrapon, N. / Lombard, V. / Henrissat, B. / Turnbull, J.E. / Czjzek, M. / Gilbert, H.J. / Bolam, D.N.
History
DepositionApr 13, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 24, 2017Provider: repository / Type: Initial release
Revision 1.1May 31, 2017Group: Structure summary
Revision 2.0Oct 25, 2017Group: Advisory / Atomic model / Category: atom_site / pdbx_unobs_or_zero_occ_atoms
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_atom_id / _atom_site.label_atom_id
Revision 2.1Dec 12, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 3.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / 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_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_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.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_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.1Jan 10, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 2-O GLYCOSAMINOGLYCAN SULFATASE
B: 2-O GLYCOSAMINOGLYCAN SULFATASE
C: 2-O GLYCOSAMINOGLYCAN SULFATASE
D: 2-O GLYCOSAMINOGLYCAN SULFATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)223,70249
Polymers219,5834
Non-polymers4,11945
Water21,1141172
1
A: 2-O GLYCOSAMINOGLYCAN SULFATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,07112
Polymers54,8961
Non-polymers1,17511
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 2-O GLYCOSAMINOGLYCAN SULFATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,13313
Polymers54,8961
Non-polymers1,23712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: 2-O GLYCOSAMINOGLYCAN SULFATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,81113
Polymers54,8961
Non-polymers91612
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: 2-O GLYCOSAMINOGLYCAN SULFATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,68711
Polymers54,8961
Non-polymers79210
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.207, 114.526, 127.293
Angle α, β, γ (deg.)90.00, 100.04, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
2-O GLYCOSAMINOGLYCAN SULFATASE


Mass: 54895.754 Da / Num. of mol.: 4 / Fragment: SULFATASE, UNP RESIDUE 13-481
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACTEROIDES THETAIOTAOMICRON (bacteria)
Strain: VPI-5482 / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8A7C8, EC: 3.1.6.18

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Sugars , 2 types, 4 molecules

#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


Type: oligosaccharide / Mass: 577.470 Da / Num. of mol.: 2 / Source method: obtained synthetically
DescriptorTypeProgram
[][a-D-GlcpNSO36SO3]{[(4+1)][a-L-4-deoxy-IdopA2SO3]{}}LINUCSPDB-CARE
#6: Sugar ChemComp-UAP / 4-deoxy-2-O-sulfo-alpha-L-threo-hex-4-enopyranuronic acid / 4-deoxy-2-O-sulfo-alpha-L-threo-hex-4-enuronic acid / 4-deoxy-2-O-sulfo-L-threo-hex-4-enuronic acid / 4-deoxy-2-O-sulfo-threo-hex-4-enuronic acid


Type: L-saccharide, alpha linking / Mass: 256.187 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O9S
IdentifierTypeProgram
b-D-4-deoxy-GlcpA2SO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 4 types, 1213 molecules

#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 33 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1172 / 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: 2.26 Å3/Da / Density % sol: 45.56 % / Description: NONE
Crystal growDetails: 14-20 % PEG 3350 0.2 M KCL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.98
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 10, 2014 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.9→46.4 Å / Num. obs: 153578 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 9
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 2.6 / % possible all: 76.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3B5Q

3b5q


Resolution: 1.9→125.34 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.948 / SU B: 3.314 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R: 0.136 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.19806 7624 5 %RANDOM
Rwork0.16028 ---
obs0.16216 145915 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.417 Å2
Baniso -1Baniso -2Baniso -3
1--0.61 Å20 Å2-0.01 Å2
2---1.3 Å20 Å2
3---1.8 Å2
Refinement stepCycle: LAST / Resolution: 1.9→125.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14417 0 242 1172 15831
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01915103
X-RAY DIFFRACTIONr_bond_other_d0.0020.0213775
X-RAY DIFFRACTIONr_angle_refined_deg1.5241.9620537
X-RAY DIFFRACTIONr_angle_other_deg0.995331791
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.25851878
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.35923.761686
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.61152276
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3261590
X-RAY DIFFRACTIONr_chiral_restr0.0910.22209
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02117130
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023460
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.351.8897461
X-RAY DIFFRACTIONr_mcbond_other1.3491.8887460
X-RAY DIFFRACTIONr_mcangle_it2.1512.8259323
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.922.1357642
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.259 530 -
Rwork0.234 10795 -
obs--99.97 %

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