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Basic information

Entry
Database: PDB / ID: 5fql
TitleInsights into Hunter syndrome from the structure of iduronate-2- sulfatase
ComponentsIDURONATE-2-SULFATASE
KeywordsHYDROLASE / HUNTER SYNDROME
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 / SAD / Resolution: 2.3 Å
AuthorsDemydchuk, M. / Hill, C.H. / Zhou, A. / Bunkoczi, G. / Stein, P.E. / Marchesan, D. / Deane, J.E. / Read, R.J.
CitationJournal: Nat Commun / Year: 2017
Title: Insights into Hunter syndrome from the structure of iduronate-2-sulfatase.
Authors: Demydchuk, M. / Hill, C.H. / Zhou, A. / Bunkoczi, G. / Stein, P.E. / Marchesan, D. / Deane, J.E. / Read, R.J.
History
DepositionDec 11, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 18, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 21, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _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 2.0Oct 23, 2019Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other
Category: atom_site / chem_comp ...atom_site / chem_comp / pdbx_database_status / struct_conn
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 / _chem_comp.type / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag
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_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.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.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
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: IDURONATE-2-SULFATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,58512
Polymers59,4351
Non-polymers3,14911
Water3,837213
1
A: IDURONATE-2-SULFATASE
hetero molecules

A: IDURONATE-2-SULFATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,17024
Polymers118,8712
Non-polymers6,29922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-y+1,-x+1,-z+2/31
Buried area11630 Å2
ΔGint-4 kcal/mol
Surface area40260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.050, 71.050, 285.879
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number151
Space group name H-MP3112

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Components

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Protein , 1 types, 1 molecules A

#1: Protein IDURONATE-2-SULFATASE / 3.1.6.13 / ALPHA-L-IDURONATE SULFATE SULFATASE / IDURSULFASE / IDURONATE 2-SULFATASE 42 KDA CHAIN / ...3.1.6.13 / ALPHA-L-IDURONATE SULFATE SULFATASE / IDURSULFASE / IDURONATE 2-SULFATASE 42 KDA CHAIN / IDURONATE 2-SULFATASE 14 KDA CHAIN


Mass: 59435.480 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): HT-1080 / Production host: HOMO SAPIENS (human) / References: UniProt: P22304, iduronate-2-sulfatase

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Sugars , 3 types, 7 molecules

#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.: 3
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.: 2
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
#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


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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Non-polymers , 3 types, 217 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 213 / 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: 3.5 Å3/Da / Density % sol: 65 % / Description: NONE
Crystal growpH: 6.1 / Details: 0.1 M MES PH=6.1 1.0 M LICL 20% PEG6K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9763, 1.475
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 13, 2008
RadiationMonochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97631
21.4751
ReflectionResolution: 2.3→35.52 Å / Num. obs: 35738 / % possible obs: 96.2 % / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Biso Wilson estimate: 46.18 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.4
Reflection shellResolution: 2.3→2.39 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.94 / Mean I/σ(I) obs: 1.9 / % possible all: 97.7

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.3→35.525 Å / SU ML: 0.29 / σ(F): 0.66 / Phase error: 25.89 / Stereochemistry target values: ML / Details: RESIDUES 444-453 ARE DISORDERED
RfactorNum. reflection% reflection
Rfree0.2081 1777 5 %
Rwork0.181 --
obs0.1824 35676 95.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→35.525 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4051 0 202 213 4466
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034417
X-RAY DIFFRACTIONf_angle_d0.6146051
X-RAY DIFFRACTIONf_dihedral_angle_d14.8622615
X-RAY DIFFRACTIONf_chiral_restr0.043683
X-RAY DIFFRACTIONf_plane_restr0.004776
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3001-2.36220.3721310.33622654X-RAY DIFFRACTION97
2.3622-2.43170.29011490.30622556X-RAY DIFFRACTION96
2.4317-2.51020.32961250.27672494X-RAY DIFFRACTION92
2.5102-2.59990.30581400.24432602X-RAY DIFFRACTION97
2.5999-2.70390.24031060.23162695X-RAY DIFFRACTION98
2.7039-2.8270.25731390.22522628X-RAY DIFFRACTION97
2.827-2.97590.27121520.20842591X-RAY DIFFRACTION96
2.9759-3.16230.24481300.19212491X-RAY DIFFRACTION92
3.1623-3.40630.20251490.18742638X-RAY DIFFRACTION97
3.4063-3.74870.19211260.16522707X-RAY DIFFRACTION98
3.7487-4.29040.15391410.14072523X-RAY DIFFRACTION93
4.2904-5.40230.17181550.132687X-RAY DIFFRACTION97
5.4023-35.52920.18991340.17242633X-RAY DIFFRACTION92
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)
11.1006-0.63770.08831.3473-0.56722.90920.01120.24350.17940.0944-0.1176-0.0907-0.3490.02790.08810.55080.14460.03130.51160.00910.483927.575627.8617125.6371
22.7451.9612-0.63425.049-2.5394.7020.19280.51210.151-0.1593-0.11230.2447-0.3492-0.4713-0.10140.66030.3132-0.00670.9947-0.00480.501612.376831.1047106.8531
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 34 THROUGH 443 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 454 THROUGH 550 )

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