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- PDB-1y1j: human formylglycine generating enzyme, sulfonic acid/desulfurated form -

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Basic information

Entry
Database: PDB / ID: 1y1j
Titlehuman formylglycine generating enzyme, sulfonic acid/desulfurated form
ComponentsC-alpha-formyglycine-generating enzyme
KeywordsOXIDOREDUCTASE / Formylglycine / multiple sulfatase deficiency / cysteine sulfenic acid
Function / homology
Function and homology information


The activation of arylsulfatases / formylglycine-generating enzyme / formylglycine-generating oxidase activity / protein oxidation / glycosphingolipid catabolic process / Glycosphingolipid catabolism / cupric ion binding / post-translational protein modification / oxidoreductase activity / endoplasmic reticulum lumen ...The activation of arylsulfatases / formylglycine-generating enzyme / formylglycine-generating oxidase activity / protein oxidation / glycosphingolipid catabolic process / Glycosphingolipid catabolism / cupric ion binding / post-translational protein modification / oxidoreductase activity / endoplasmic reticulum lumen / endoplasmic reticulum / identical protein binding
Similarity search - Function
paralog of FGE (formylglycine-generating enzyme) / paralog of FGE (formylglycine-generating enzyme) / : / Sulfatase-modifying factor enzyme / Sulfatase-modifying factor enzyme 1 / Sulfatase-modifying factor enzyme superfamily / C-type lectin fold / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
: / Formylglycine-generating enzyme
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsRudolph, M.G. / Dickmanns, A. / Ficner, R.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2005
Title: Molecular basis for multiple sulfatase deficiency and mechanism for formylglycine generation of the human formylglycine-generating enzyme.
Authors: Dierks, T. / Dickmanns, A. / Preusser-Kunze, A. / Schmidt, B. / Mariappan, M. / von Figura, K. / Ficner, R. / Rudolph, M.G.
History
DepositionNov 18, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 31, 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 / 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.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 / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
X: C-alpha-formyglycine-generating enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6835
Polymers34,9571
Non-polymers7264
Water8,485471
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.180, 109.655, 43.484
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein C-alpha-formyglycine-generating enzyme / FGE


Mass: 34956.645 Da / Num. of mol.: 1 / Fragment: residues 73-383
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell (production host): fibrosarcoma tumor cells / Cell line (production host): HT1080 / Production host: Homo sapiens (human) / References: GenBank: 30840149, UniProt: Q8NBK3*PLUS
#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.: 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
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-CXS / 3-CYCLOHEXYL-1-PROPYLSULFONIC ACID


Mass: 221.317 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H19NO3S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 471 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.12 Å3/Da / Density % sol: 41.99 %

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Data collection

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.55→54.88 Å / Num. obs: 35522 / % possible obs: 80.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Rsym value: 0.043 / Net I/σ(I): 26.5
Reflection shellResolution: 1.55→1.61 Å / Redundancy: 1.25 % / Mean I/σ(I) obs: 3.3 / Num. unique all: 820 / Rsym value: 0.162 / % possible all: 19.1

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Processing

SoftwareName: REFMAC / Version: 5.2.0005 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→41.1 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.946 / SU B: 1.499 / SU ML: 0.054 / Cross valid method: THROUGHOUT / ESU R: 0.093 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19301 1722 4.9 %RANDOM
Rwork0.15803 ---
obs0.1597 33756 81.21 %-
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: 13.348 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å20 Å20 Å2
2--0.43 Å20 Å2
3----0.61 Å2
Refinement stepCycle: LAST / Resolution: 1.55→41.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2180 0 44 471 2695
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0212359
X-RAY DIFFRACTIONr_bond_other_d0.0010.021988
X-RAY DIFFRACTIONr_angle_refined_deg1.3411.943228
X-RAY DIFFRACTIONr_angle_other_deg0.79534647
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4755275
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.72623.621116
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.83615343
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2091514
X-RAY DIFFRACTIONr_chiral_restr0.0790.2328
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022620
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02498
X-RAY DIFFRACTIONr_nbd_refined0.2030.2504
X-RAY DIFFRACTIONr_nbd_other0.1950.22073
X-RAY DIFFRACTIONr_nbtor_refined0.1860.21159
X-RAY DIFFRACTIONr_nbtor_other0.0830.21196
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1650.2361
X-RAY DIFFRACTIONr_metal_ion_refined0.0780.210
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1910.216
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1880.264
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2230.241
X-RAY DIFFRACTIONr_mcbond_it0.7841.51424
X-RAY DIFFRACTIONr_mcbond_other0.1871.5560
X-RAY DIFFRACTIONr_mcangle_it1.20622252
X-RAY DIFFRACTIONr_scbond_it1.82531108
X-RAY DIFFRACTIONr_scangle_it2.7374.5976
LS refinement shellResolution: 1.553→1.594 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.243 22 -
Rwork0.276 481 -
obs--15.94 %

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