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- PDB-1y4j: Crystal structure of the paralogue of the human formylglycine gen... -

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Basic information

Entry
Database: PDB / ID: 1y4j
TitleCrystal structure of the paralogue of the human formylglycine generating enzyme
ComponentsSulfatase modifying factor 2
KeywordsSUGAR BINDING PROTEIN / formylglycine / sulfatases / multiple sulfatase deficiency / homodimer / duf323
Function / homology
Function and homology information


Glycosphingolipid metabolism / The activation of arylsulfatases / glycosphingolipid metabolic process / post-translational protein modification / endoplasmic reticulum lumen / endoplasmic reticulum / metal ion 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
Inactive C-alpha-formylglycine-generating enzyme 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MIRAS / Resolution: 1.864 Å
AuthorsDickmanns, A. / Rudolph, M.G. / Ficner, R.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Crystal Structure of Human pFGE, the Paralog of the C{alpha}-formylglycine-generating Enzyme
Authors: Dickmanns, A. / Schmidt, B. / Rudolph, M.G. / Mariappan, M. / Dierks, T. / von Figura, K. / Ficner, R.
History
DepositionDec 1, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 8, 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 1.3Nov 26, 2014Group: Other
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / 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_validate_chiral / pdbx_validate_close_contact / 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 / _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_validate_chiral.auth_asym_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _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

Downloads & links

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Assembly

Deposited unit
A: Sulfatase modifying factor 2
B: Sulfatase modifying factor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,8239
Polymers64,5502
Non-polymers1,2737
Water10,124562
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4030 Å2
ΔGint-63 kcal/mol
Surface area23300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.078, 100.750, 62.704
Angle α, β, γ (deg.)90.00, 101.68, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly could be the dimer in the asymmetric unit

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Sulfatase modifying factor 2 / C-alpha-formyglycine- generating enzyme 2 / UNQ1968/PRO4500


Mass: 32274.883 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: HT1080 cells / Gene: SUMF2 / References: UniProt: Q8NBJ7

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Sugars , 2 types, 2 molecules

#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#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, 567 molecules

#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 562 / 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: 2.26 Å3/Da / Density % sol: 45.48 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8
Details: Tris/HCl, MPD, CaCl2, PEG8000, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 26, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.86→50 Å / Num. obs: 47438 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 29.4 Å2 / Rsym value: 0.055 / Net I/σ(I): 22.7
Reflection shellResolution: 1.86→1.93 Å / Redundancy: 3 % / Mean I/σ(I) obs: 1.8 / Num. unique all: 4141 / Rsym value: 0.586 / % possible all: 87.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RESOLVEphasing
RefinementMethod to determine structure: MIRAS / Resolution: 1.864→32 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.949 / SU B: 3.427 / SU ML: 0.102 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.144 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20548 2387 5 %RANDOM
Rwork0.16996 ---
obs0.17185 45026 99.35 %-
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: 28.299 Å2
Baniso -1Baniso -2Baniso -3
1-1.29 Å20 Å21.23 Å2
2---0.61 Å20 Å2
3----0.18 Å2
Refinement stepCycle: LAST / Resolution: 1.864→32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4283 0 78 562 4923
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0214558
X-RAY DIFFRACTIONr_bond_other_d0.0020.023945
X-RAY DIFFRACTIONr_angle_refined_deg1.3381.9356190
X-RAY DIFFRACTIONr_angle_other_deg0.81139137
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6065531
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.33922.757243
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.8515698
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9481549
X-RAY DIFFRACTIONr_chiral_restr0.0790.2612
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025114
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021047
X-RAY DIFFRACTIONr_nbd_refined0.2030.2889
X-RAY DIFFRACTIONr_nbd_other0.2020.24174
X-RAY DIFFRACTIONr_nbtor_refined0.1840.22231
X-RAY DIFFRACTIONr_nbtor_other0.0850.22437
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.2454
X-RAY DIFFRACTIONr_metal_ion_refined0.0910.24
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1420.221
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2570.266
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1740.222
X-RAY DIFFRACTIONr_mcbond_it0.9251.52738
X-RAY DIFFRACTIONr_mcbond_other0.1851.51086
X-RAY DIFFRACTIONr_mcangle_it1.41324257
X-RAY DIFFRACTIONr_scbond_it1.90632163
X-RAY DIFFRACTIONr_scangle_it2.8574.51933
LS refinement shellResolution: 1.86→1.913 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 155 -
Rwork0.272 3065 -
obs--92.16 %

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