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- PDB-6ioz: Structural insights of idursulfase beta -

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Basic information

Entry
Database: PDB / ID: 6ioz
TitleStructural insights of idursulfase beta
ComponentsIduronate 2-sulfatase
KeywordsHYDROLASE / IDURSULFASE BETA / ALPHA-L-IDURONATE SULFATE SULFATASE / IDURONATE 2-SULFATASE 42KDA CHAIN / IDURONATE 2-SULFATASE 14KDA CHAIN
Function / homology
Function and homology information


iduronate-2-sulfatase / MPS II - Hunter syndrome / iduronate-2-sulfatase activity / dermatan sulfate catabolic process / glycosaminoglycan catabolic process / CS/DS degradation / heparan sulfate proteoglycan catabolic process / HS-GAG degradation / lysosomal lumen / lysosome ...iduronate-2-sulfatase / MPS II - Hunter syndrome / iduronate-2-sulfatase activity / dermatan sulfate catabolic process / glycosaminoglycan catabolic process / CS/DS degradation / heparan sulfate proteoglycan catabolic process / HS-GAG degradation / lysosomal lumen / lysosome / calcium ion binding / cytoplasm
Similarity search - Function
Iduronate-2-sulfatase / Sulfatases signature 2. / Sulfatases signature 1. / Sulfatase, conserved site / Sulfatase, N-terminal / Sulfatase / Alkaline-phosphatase-like, core domain superfamily
Similarity search - Domain/homology
Iduronate 2-sulfatase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsKim, H. / Kim, D. / Hong, J. / Lee, K. / Seo, J. / Oh, B.H.
CitationJournal: To Be Published
Title: Structural insights of idursulfase beta
Authors: Kim, H. / Kim, D. / Hong, J. / Lee, K. / Seo, J. / Oh, B.H.
History
DepositionNov 1, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 28, 2018Provider: repository / Type: Initial release
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 / 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.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_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_role / _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 2.1Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Iduronate 2-sulfatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,5139
Polymers58,6171
Non-polymers2,8978
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, size exclusion, mass spectrometry, mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3620 Å2
ΔGint40 kcal/mol
Surface area21540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.825, 70.825, 285.697
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number151
Space group name H-MP3112

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Components

#1: Protein Iduronate 2-sulfatase / Alpha-L-iduronate sulfate sulfatase / Idursulfase


Mass: 58616.695 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IDS, SIDS / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P22304, iduronate-2-sulfatase
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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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: 3.66 Å3/Da / Density % sol: 66.43 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 1.0 M LiCl 0.1M MES (pH 6.0) 20% w/v PEG 6K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.9794 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 12, 2018
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 12919 / % possible obs: 83.2 % / Redundancy: 6.6 % / Biso Wilson estimate: 65.7 Å2 / Rmerge(I) obs: 0.149 / Rpim(I) all: 0.049 / Rrim(I) all: 0.158 / Χ2: 3.718 / Net I/σ(I): 9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.1-3.152.60.3164120.3280.1680.3631.53756.1
3.15-3.212.80.3254500.5910.1710.3721.95658.7
3.21-3.273.20.3034680.650.1420.3391.82560.5
3.27-3.343.10.2994990.8040.1460.3361.74165.1
3.34-3.413.20.2825430.7490.1410.3192.00370.9
3.41-3.493.30.2585070.9240.1170.2862.37566.6
3.49-3.584.20.2686100.8910.1080.2912.48178
3.58-3.684.70.2626240.8920.1050.2852.58382.5
3.68-3.784.80.2446330.9430.0960.2632.53383.5
3.78-3.915.50.2376570.9530.0870.2543.01885
3.91-4.045.90.226980.9730.080.2363.26290.3
4.04-4.216.20.2077220.9850.0730.223.28891.9
4.21-4.46.70.1957190.9910.0680.2073.71693.6
4.4-4.636.90.1877130.9770.0650.1994.23892.5
4.63-4.9290.1817470.9880.0560.194.2496.1
4.92-5.39.10.1787520.9750.0560.1873.92997.2
5.3-5.839.20.1737620.9890.0530.1813.97496.1
5.83-6.679.30.1567670.9870.0490.1643.87397.7
6.67-8.411.20.1327880.9940.0390.1374.20698.3
8.4-5011.40.0998480.9940.030.1044.997.7

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data scaling
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5FQL

5fql


Resolution: 3.1→47.616 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.66 / Phase error: 28.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2431 643 5.01 %
Rwork0.1972 12189 -
obs0.1996 12832 83.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 219.34 Å2 / Biso mean: 85.6507 Å2 / Biso min: 32.27 Å2
Refinement stepCycle: final / Resolution: 3.1→47.616 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4009 0 357 0 4366
Biso mean--138.57 --
Num. residues----501
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044362
X-RAY DIFFRACTIONf_angle_d0.7875971
X-RAY DIFFRACTIONf_chiral_restr0.057671
X-RAY DIFFRACTIONf_plane_restr0.004766
X-RAY DIFFRACTIONf_dihedral_angle_d14.3052581
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.1002-3.33950.3224910.29311743183461
3.3395-3.67540.27711160.22552157227375
3.6754-4.2070.2361310.17172561269288
4.207-5.29920.20321470.16812762290995
5.2992-47.62180.24261580.19822966312498

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