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- PDB-2hi8: human formylglycine generating enzyme, C336S mutant, bromide co-c... -

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Basic information

Entry
Database: PDB / ID: 2hi8
Titlehuman formylglycine generating enzyme, C336S mutant, bromide co-crystallization
Components
  • CTPSR
  • Sulfatase-modifying factor 1
KeywordsHYDROLASE ACTIVATOR / PROTEIN BINDING / formylglycin generation / 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. / Sulfatase, conserved site / Sulfatase, N-terminal ...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
BROMIDE ION / Arylsulfatase A / Formylglycine-generating enzyme
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å
AuthorsRudolph, M.G. / Roeser, D.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2007
Title: Probing the oxygen-binding site of the human formylglycine-generating enzyme using halide ions.
Authors: Roeser, D. / Schmidt, B. / Preusser-Kunze, A. / Rudolph, M.G.
History
DepositionJun 29, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 1, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 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 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,41321
Polymers32,6742
Non-polymers1,73919
Water7,855436
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3410 Å2
ΔGint-40 kcal/mol
Surface area11800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.158, 108.792, 43.057
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-1015-

BR

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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 / Production host: Homo sapiens (human) / References: UniProt: Q8NBK3
#2: Protein/peptide CTPSR


Mass: 563.648 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: The peptide was chemically synthesized. / References: UniProt: P15289*PLUS
#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 , 4 types, 454 molecules

#4: Chemical
ChemComp-BR / BROMIDE ION / Bromide


Mass: 79.904 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: Br
#5: Chemical ChemComp-CA / CALCIUM ION


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


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


Mass: 18.015 Da / Num. of mol.: 436 / 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: 2.19 Å3/Da / Density % sol: 43.84 %
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: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.81 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 30, 2006
RadiationMonochromator: Si [111], horizontally focussing / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.81 Å / Relative weight: 1
ReflectionResolution: 1.63→50 Å / Num. obs: 35818 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rsym value: 0.075 / Net I/σ(I): 15
Reflection shellResolution: 1.63→1.69 Å / Redundancy: 3 % / Mean I/σ(I) obs: 3 / Num. unique all: 2823 / Rsym value: 0.396 / % possible all: 78.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2afy

2afy


Resolution: 1.64→27.2 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.946 / SU B: 1.768 / SU ML: 0.06 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.09 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. The close contacts are partial occupancy contacts, where the occupancies of the clashing atoms sum up to one.
RfactorNum. reflection% reflectionSelection details
Rfree0.19067 1726 4.8 %RANDOM
Rwork0.15338 ---
obs0.15516 33959 99.04 %-
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: 12.435 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å20 Å20 Å2
2--0.23 Å20 Å2
3----0.39 Å2
Refinement stepCycle: LAST / Resolution: 1.64→27.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2214 0 46 436 2696
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0212431
X-RAY DIFFRACTIONr_bond_other_d0.0020.021675
X-RAY DIFFRACTIONr_angle_refined_deg1.311.9383333
X-RAY DIFFRACTIONr_angle_other_deg2.0743.0024046
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4585296
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.46123.415123
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.13315364
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7971517
X-RAY DIFFRACTIONr_chiral_restr0.070.2335
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022737
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02524
X-RAY DIFFRACTIONr_nbd_refined0.2220.2610
X-RAY DIFFRACTIONr_nbd_other0.230.21995
X-RAY DIFFRACTIONr_nbtor_refined0.1940.21210
X-RAY DIFFRACTIONr_nbtor_other0.0960.21248
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.2381
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.10.210
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3970.226
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3470.244
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2010.234
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7511.51460
X-RAY DIFFRACTIONr_mcbond_other0.0771.5569
X-RAY DIFFRACTIONr_mcangle_it1.12822322
X-RAY DIFFRACTIONr_scbond_it1.66731137
X-RAY DIFFRACTIONr_scangle_it2.5994.51002
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.64→1.682 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 113 -
Rwork0.239 2201 -
obs--88.35 %

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