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- PDB-4mhx: Crystal Structure of Sulfamidase -

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Basic information

Entry
Database: PDB / ID: 4mhx
TitleCrystal Structure of Sulfamidase
ComponentsN-sulphoglucosamine sulphohydrolase
KeywordsHYDROLASE / sulfatase fold / heparan / heparin / lysosome
Function / homology
Function and homology information


N-sulfoglucosamine sulfohydrolase / N-sulfoglucosamine sulfohydrolase activity / MPS IIIA - Sanfilippo syndrome A / glycosaminoglycan catabolic process / heparan sulfate proteoglycan catabolic process / sulfuric ester hydrolase activity / HS-GAG degradation / motor behavior / lysosomal lumen / determination of adult lifespan ...N-sulfoglucosamine sulfohydrolase / N-sulfoglucosamine sulfohydrolase activity / MPS IIIA - Sanfilippo syndrome A / glycosaminoglycan catabolic process / heparan sulfate proteoglycan catabolic process / sulfuric ester hydrolase activity / HS-GAG degradation / motor behavior / lysosomal lumen / determination of adult lifespan / lysosome / extracellular exosome / metal ion binding
Similarity search - Function
N-sulphoglucosamine sulphohydrolase, C-terminal / N-sulphoglucosamine sulphohydrolase, C-terminal / Sulfatases signature 2. / Sulfatases signature 1. / Sulfatase, conserved site / Sulfatase, N-terminal / Sulfatase / Alkaline Phosphatase, subunit A / Alkaline Phosphatase, subunit A / Alkaline-phosphatase-like, core domain superfamily ...N-sulphoglucosamine sulphohydrolase, C-terminal / N-sulphoglucosamine sulphohydrolase, C-terminal / Sulfatases signature 2. / Sulfatases signature 1. / Sulfatase, conserved site / 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
N-sulphoglucosamine sulphohydrolase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsSidhu, N.S. / Uson, I. / Schreiber, K. / Proepper, K. / Becker, S. / Gaertner, J. / Kraetzner, R. / Steinfeld, R. / Sheldrick, G.M.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Structure of sulfamidase provides insight into the molecular pathology of mucopolysaccharidosis IIIA.
Authors: Sidhu, N.S. / Schreiber, K. / Propper, K. / Becker, S. / Uson, I. / Sheldrick, G.M. / Gartner, J. / Kratzner, R. / Steinfeld, R.
History
DepositionAug 30, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 14, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 9, 2015Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / 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_ref_seq_dif / 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_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_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_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jun 2, 2021Group: Source and taxonomy / Structure summary / Category: chem_comp / entity_src_gen
Item: _chem_comp.pdbx_synonyms / _entity_src_gen.host_org_common_name ..._chem_comp.pdbx_synonyms / _entity_src_gen.host_org_common_name / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: N-sulphoglucosamine sulphohydrolase
B: N-sulphoglucosamine sulphohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,53614
Polymers115,8242
Non-polymers2,71112
Water3,693205
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7970 Å2
ΔGint-26 kcal/mol
Surface area33980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.380, 107.900, 79.790
Angle α, β, γ (deg.)90.00, 104.07, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A22 - 69
2010B22 - 69
1020A71 - 502
2020B71 - 502

NCS ensembles :
ID
1
2
Detailsbiological unit is the same as asym.

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein N-sulphoglucosamine sulphohydrolase / Sulfoglucosamine sulfamidase / Sulphamidase


Mass: 57912.199 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SGSH, HSS / Cell line (production host): HEK 293 / Production host: Homo sapiens (human)
References: UniProt: P51688, N-sulfoglucosamine sulfohydrolase

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Sugars , 2 types, 8 molecules

#2: 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.: 4
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: 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.: 4
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, 209 molecules

#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 205 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsAUTHORS STATE THAT THE CYS->FGP CONFLICT IS DUE TO A NATURAL REACTION THAT FIRST CHANGED CYS TO A ...AUTHORS STATE THAT THE CYS->FGP CONFLICT IS DUE TO A NATURAL REACTION THAT FIRST CHANGED CYS TO A FORMYLGLYCINE RESIDUE. THE LATTER THEN APPARENTLY PICKED UP A PHOSPHATE FROM THE PURIFICATION BUFFER TO BECOME FGP

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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: 2.21 Å3/Da / Density % sol: 44.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 25% (w/v) polyethylene glycol (PEG) 3350, 200 mM MgCl2 and 100 mM HEPES buffer, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99989 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 23, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99989 Å / Relative weight: 1
ReflectionHighest resolution: 1.99 Å / Num. obs: 134186 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 45.081 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 7.83
Reflection shell

Rmerge(I) obs: 0.011 / Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Mean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.99-2.041.0626028898688.8
2.04-2.11.4633604974699.7
2.1-2.161.8532844943999.8
2.16-2.232.331862922899.7
2.23-2.32.8529909898799.7
2.3-2.383.4628144864299.8
2.38-2.474.229263832099.7
2.47-2.575.0828542806999.8
2.57-2.696.2226772770499.8
2.69-2.827.3624251735699.7
2.82-2.978.9723683702099.7
2.97-3.1511.2423565659899.7
3.15-3.3713.4621910625599.6
3.37-3.6415.6819110576398.8
3.64-3.9818.2117505528499.2
3.98-4.4520.0516605477698.9
4.45-5.1420.3114020421498.9
5.14-6.320.1111556355198.5
6.3-8.9121.759530277199.3
8.9122.624760147797.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å44.26 Å
Translation2.5 Å44.26 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.3.0phasing
DMphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
XDSdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→44.3 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.956 / WRfactor Rfree: 0.2376 / WRfactor Rwork: 0.1965 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.7948 / SU B: 12.694 / SU ML: 0.161 / SU R Cruickshank DPI: 0.1937 / SU Rfree: 0.1648 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.194 / ESU R Free: 0.165 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2299 3447 5.1 %RANDOM
Rwork0.192 ---
obs0.1939 67884 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 110.49 Å2 / Biso mean: 44.9877 Å2 / Biso min: 20.77 Å2
Baniso -1Baniso -2Baniso -3
1-2.43 Å2-0 Å2-1.44 Å2
2--0.07 Å20 Å2
3----1.91 Å2
Refinement stepCycle: LAST / Resolution: 2→44.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7591 0 172 205 7968
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0198039
X-RAY DIFFRACTIONr_bond_other_d0.0040.027262
X-RAY DIFFRACTIONr_angle_refined_deg1.5641.97111027
X-RAY DIFFRACTIONr_angle_other_deg1.0273.00116597
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3675965
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.48523.14363
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.06151135
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4491550
X-RAY DIFFRACTIONr_chiral_restr0.0870.21210
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0219116
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021959
X-RAY DIFFRACTIONr_mcbond_it1.6642.5063867
X-RAY DIFFRACTIONr_mcbond_other1.6642.5063866
X-RAY DIFFRACTIONr_mcangle_it2.4853.7584821
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A19010.09
12B19010.09
21A247350.07
22B247350.07
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.4 240 -
Rwork0.389 4699 -
all-4939 -
obs--99.12 %
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)
10.55130.37820.47011.65290.22221.20940.0702-0.04240.03340.3712-0.0778-0.18610.01630.13460.00760.1232-0.05-0.01280.15680.03140.09293.894212.234867.1744
21.5592-1.30443.17882.1916-2.62568.66440.2537-0.09520.05630.3365-0.21470.37930.81-0.4353-0.03890.348-0.17090.20070.2767-0.05590.1961-16.43255.779269.1613
32.9413-0.59840.2811.67610.06921.24190.1262-0.0915-0.19170.4347-0.0452-0.19470.45040.1623-0.0810.2991-0.0021-0.06840.1001-0.01030.10682.5631-11.655461.4295
40.75352.12450.408811.7641.60836.83310.1498-0.25020.00420.9906-0.28081.00031.0388-0.43960.1310.217-0.07710.11570.23390.01910.1937-15.2063-15.188649.3141
50.81710.34560.40371.25860.42020.9489-0.10490.06920.1081-0.2764-0.0080.2526-0.34-0.11360.11290.17590.0047-0.03150.14150.01110.1201-15.75852.206122.8712
60.87140.4970.23231.80843.58039.7621-0.32010.14430.0328-0.16350.2545-0.0725-0.29881.37890.06560.333-0.19540.01770.47980.10780.11844.43758.70721.3835
71.99641.6990.03182.82970.21671.7188-0.0230.1582-0.204-0.04550.0823-0.24880.25230.2578-0.05920.04110.04070.00850.13840.00340.1145-1.0303-15.07232.3851
84.8396-5.47361.08666.577-3.00679.07560.32920.28890.5825-0.5131-0.5945-0.78030.76881.54960.26520.12090.06210.05060.4129-0.02490.389214.5461-5.229343.7277
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A22 - 327
2X-RAY DIFFRACTION2A328 - 358
3X-RAY DIFFRACTION3A359 - 477
4X-RAY DIFFRACTION4A478 - 504
5X-RAY DIFFRACTION5B22 - 327
6X-RAY DIFFRACTION6B328 - 358
7X-RAY DIFFRACTION7B359 - 477
8X-RAY DIFFRACTION8B478 - 503

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