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- PDB-2aij: Formylglycine generating enzyme C336S mutant covalently bound to ... -

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Basic information

Entry
Database: PDB / ID: 2aij
TitleFormylglycine generating enzyme C336S mutant covalently bound to substrate peptide CTPSR
Components
  • CTPSR peptide from Arylsulfatase A
  • Sulfatase modifying factor 1
KeywordsHYDROLASE ACTIVATOR / PROTEIN BINDING / formylglycine / post-translational modification / endoplasmic reticulum / sulfatase
Function / homology
Function and homology information


cerebroside-sulfatase / cerebroside-sulfatase activity / The activation of arylsulfatases / formylglycine-generating enzyme / sulfuric ester hydrolase activity / arylsulfatase activity / formylglycine-generating oxidase activity / protein oxidation / glycosphingolipid catabolic process / Glycosphingolipid catabolism ...cerebroside-sulfatase / cerebroside-sulfatase activity / The activation of arylsulfatases / formylglycine-generating enzyme / sulfuric ester hydrolase activity / arylsulfatase activity / formylglycine-generating oxidase activity / protein oxidation / glycosphingolipid catabolic process / Glycosphingolipid catabolism / cupric ion binding / lysosomal lumen / post-translational protein modification / lipid metabolic process / azurophil granule lumen / oxidoreductase activity / lysosome / endoplasmic reticulum lumen / calcium ion binding / Neutrophil degranulation / endoplasmic reticulum / extracellular exosome / extracellular region / identical protein binding / membrane
Similarity search - Function
C-terminal region of aryl-sulfatase / paralog of FGE (formylglycine-generating enzyme) / paralog of FGE (formylglycine-generating enzyme) / : / Sulfatases signature 2. / : / Sulfatase-modifying factor enzyme / Sulfatase-modifying factor enzyme 1-like domain / Sulfatases signature 1. / Sulfatase-modifying factor enzyme superfamily ...C-terminal region of aryl-sulfatase / paralog of FGE (formylglycine-generating enzyme) / paralog of FGE (formylglycine-generating enzyme) / : / Sulfatases signature 2. / : / Sulfatase-modifying factor enzyme / Sulfatase-modifying factor enzyme 1-like domain / Sulfatases signature 1. / Sulfatase-modifying factor enzyme superfamily / Sulfatase, conserved site / Sulfatase, N-terminal / Sulfatase / Alkaline-phosphatase-like, core domain superfamily / C-type lectin fold / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Arylsulfatase A / Formylglycine-generating enzyme
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsRoeser, D. / Rudolph, M.G.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2006
Title: A general binding mechanism for all human sulfatases by the formylglycine-generating enzyme
Authors: Roeser, D. / Preusser-Kunze, A. / Schmidt, B. / Gasow, K. / Wittmann, J.G. / Dierks, T. / von Figura, K. / Rudolph, M.G.
History
DepositionJul 29, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 13, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
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 / pdbx_struct_special_symmetry / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.label_asym_id ..._atom_site.auth_asym_id / _atom_site.label_asym_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _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_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_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_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_struct_special_symmetry.label_asym_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
Revision 2.1Nov 10, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 2.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
X: Sulfatase modifying factor 1
P: CTPSR peptide from Arylsulfatase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2146
Polymers32,6742
Non-polymers5404
Water9,566531
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1740 Å2
ΔGint-38 kcal/mol
Surface area11910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.640, 109.592, 43.456
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11X-1296-

HOH

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Components

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Protein / Protein/peptide / Sugars , 3 types, 3 molecules XP

#1: Protein Sulfatase modifying factor 1 / C-alpha-formyglycine- generating enzyme 1


Mass: 32110.613 Da / Num. of mol.: 1 / Fragment: residues 86-371 / Mutation: C336S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell (production host): fibrosarcoma cells / Cell line (production host): HT1080 / Production host: Homo sapiens (human) / References: UniProt: Q8NBK3
#2: Protein/peptide CTPSR peptide from Arylsulfatase A


Mass: 563.648 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: chemically synthesized / References: UniProt: P15289
#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.: 1
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

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Non-polymers , 3 types, 534 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 531 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.25 Å3/Da / Density % sol: 45.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: PEG 4000, Calcium chloride, TRIS, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 7, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.55→30 Å / Num. obs: 42603 / % possible obs: 97.5 % / Redundancy: 4.3 % / Biso Wilson estimate: 16.43 Å2 / Rsym value: 0.033 / Net I/σ(I): 41.2
Reflection shellResolution: 1.55→1.61 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 5.6 / Rsym value: 0.181 / % possible all: 89.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0009refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1Y1E

1y1e


Resolution: 1.55→24.5 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.293 / SU ML: 0.047 / Cross valid method: THROUGHOUT / ESU R: 0.072 / ESU R Free: 0.075 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17777 2063 4.8 %RANDOM
Rwork0.14442 ---
obs0.14601 40491 97.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 18.218 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20 Å20 Å2
2--0.44 Å20 Å2
3----0.57 Å2
Refinement stepCycle: LAST / Resolution: 1.55→24.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2214 0 31 531 2776
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0212389
X-RAY DIFFRACTIONr_bond_other_d0.0020.022008
X-RAY DIFFRACTIONr_angle_refined_deg1.4081.9373265
X-RAY DIFFRACTIONr_angle_other_deg0.84334695
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4325278
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.02323.529119
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.41815354
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7611515
X-RAY DIFFRACTIONr_chiral_restr0.090.2330
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022656
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02507
X-RAY DIFFRACTIONr_nbd_refined0.2170.2525
X-RAY DIFFRACTIONr_nbd_other0.2040.22142
X-RAY DIFFRACTIONr_nbtor_refined0.1880.21187
X-RAY DIFFRACTIONr_nbtor_other0.0850.21216
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.2394
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0830.29
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1670.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2050.243
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1920.247
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9061.51447
X-RAY DIFFRACTIONr_mcbond_other0.2311.5566
X-RAY DIFFRACTIONr_mcangle_it1.37422283
X-RAY DIFFRACTIONr_scbond_it1.93231119
X-RAY DIFFRACTIONr_scangle_it2.8954.5982
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.548→1.588 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.255 157 -
Rwork0.203 2612 -
obs--87.79 %

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