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

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Basic information

Entry
Database: PDB / ID: 2aik
TitleFormylglycine generating enzyme C336S mutant covalently bound to substrate peptide LCTPSRA
Components
  • LCTPSRA 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 / arylsulfatase activity / formylglycine-generating oxidase activity / sulfuric ester hydrolase activity / protein oxidation / glycosphingolipid catabolic process / Glycosphingolipid catabolism ...cerebroside-sulfatase / cerebroside-sulfatase activity / The activation of arylsulfatases / formylglycine-generating enzyme / arylsulfatase activity / formylglycine-generating oxidase activity / sulfuric ester hydrolase activity / protein oxidation / glycosphingolipid catabolic process / Glycosphingolipid catabolism / cupric ion binding / post-translational protein modification / lysosomal lumen / lipid metabolic process / azurophil granule lumen / lysosome / oxidoreductase activity / endoplasmic reticulum lumen / calcium ion binding / Neutrophil degranulation / endoplasmic reticulum / extracellular exosome / extracellular region / identical protein binding
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 / Sulfatase-modifying factor enzyme superfamily / Sulfatases signature 1. ...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 / Sulfatase-modifying factor enzyme superfamily / Sulfatases signature 1. / 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: 1.73 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 / 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 / _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 16, 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: LCTPSRA peptide from Arylsulfatase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3996
Polymers32,8582
Non-polymers5404
Water8,917495
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1920 Å2
ΔGint-38 kcal/mol
Surface area11880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.719, 109.517, 43.520
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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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 LCTPSRA peptide from Arylsulfatase A


Mass: 747.884 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, 498 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.: 495 / 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: 45.39 %
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: Jul 20, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.73→30 Å / Num. obs: 31093 / % possible obs: 97.8 % / Redundancy: 10.2 % / Rsym value: 0.071 / Net I/σ(I): 29.9
Reflection shellResolution: 1.73→1.79 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 1.8 / Rsym value: 0.373 / % possible all: 87

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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: 1.73→29.71 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.956 / SU B: 1.785 / SU ML: 0.059 / Cross valid method: THROUGHOUT / ESU R: 0.097 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17427 1503 4.8 %RANDOM
Rwork0.14068 ---
obs0.14228 29545 98.43 %-
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: 22.391 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20 Å20 Å2
2--0.63 Å20 Å2
3----0.67 Å2
Refinement stepCycle: LAST / Resolution: 1.73→29.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2222 0 31 495 2748
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0212388
X-RAY DIFFRACTIONr_bond_other_d0.0020.022013
X-RAY DIFFRACTIONr_angle_refined_deg1.341.9383263
X-RAY DIFFRACTIONr_angle_other_deg0.82634706
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5585279
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.0623.559118
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.19515355
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9011515
X-RAY DIFFRACTIONr_chiral_restr0.0850.2331
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022655
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02504
X-RAY DIFFRACTIONr_nbd_refined0.2060.2496
X-RAY DIFFRACTIONr_nbd_other0.1970.22160
X-RAY DIFFRACTIONr_nbtor_refined0.1830.21170
X-RAY DIFFRACTIONr_nbtor_other0.0830.21216
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1820.2367
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0780.210
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1140.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1810.242
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.20.244
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9351.51455
X-RAY DIFFRACTIONr_mcbond_other0.2261.5568
X-RAY DIFFRACTIONr_mcangle_it1.38922288
X-RAY DIFFRACTIONr_scbond_it1.95431114
X-RAY DIFFRACTIONr_scangle_it2.8974.5975
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.731→1.776 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.259 98 -
Rwork0.2 2010 -
obs--91.85 %

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