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- PDB-6s07: Structure of formylglycine-generating enzyme at 1.04 A in complex... -

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Basic information

Entry
Database: PDB / ID: 6s07
TitleStructure of formylglycine-generating enzyme at 1.04 A in complex with copper and substrate reveals an acidic pocket for binding and acti-vation of molecular oxygen.
Components
  • Abz-ALA-THR-THR-PRO-LEU-CYS-GLY-PRO-SER-ARG-ALA-SER-ILE-LEU-SER-GLY-ARG
  • Formylglycine-generating enzyme
KeywordsTRANSFERASE / Formylglycine-generating enzyme / complex / substrate analog / copper
Function / homology
Function and homology information


N-acetylglucosamine-6-sulfatase activity / formylglycine-generating enzyme / formylglycine-generating oxidase activity / protein oxidation / glycosaminoglycan binding / cuprous ion binding / post-translational protein modification / 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 / Sulfatase, N-terminal / Sulfatase / Alkaline-phosphatase-like, core domain superfamily / C-type lectin fold / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
COPPER (I) ION / Formylglycine-generating enzyme / Sulfatase
Similarity search - Component
Biological speciesThermomonospora curvata (bacteria)
Thermomonospora curvata DSM 43183 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.04 Å
AuthorsLeisinger, F. / Miarzlou, D.A. / Seebeck, F.P.
Funding support Switzerland, 2items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
European Research CouncilERC-2013- StG 336559 Switzerland
CitationJournal: Chem Sci / Year: 2019
Title: Structure of formylglycine-generating enzyme in complex with copper and a substrate reveals an acidic pocket for binding and activation of molecular oxygen.
Authors: Miarzlou, D.A. / Leisinger, F. / Joss, D. / Haussinger, D. / Seebeck, F.P.
History
DepositionJun 14, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 26, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 2.0Nov 15, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_rmsd_angle / struct_conn / struct_conn_type
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn_type.id
Revision 2.1Jan 24, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Formylglycine-generating enzyme
C: Abz-ALA-THR-THR-PRO-LEU-CYS-GLY-PRO-SER-ARG-ALA-SER-ILE-LEU-SER-GLY-ARG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1676
Polymers34,9882
Non-polymers1794
Water5,296294
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2290 Å2
ΔGint-42 kcal/mol
Surface area13910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.409, 71.939, 76.733
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AC

#1: Protein Formylglycine-generating enzyme / FGE


Mass: 33336.852 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermomonospora curvata (strain ATCC 19995 / DSM 43183 / JCM 3096 / NBRC 15933 / NCIMB 10081 / Henssen B9) (bacteria)
Strain: ATCC 19995 / DSM 43183 / JCM 3096 / NBRC 15933 / NCIMB 10081 / Henssen B9
Gene: Tcur_4811 / Production host: Escherichia coli (E. coli) / Strain (production host): B / BL21-DE3 [Korea]
References: UniProt: D1A7C3, formylglycine-generating enzyme
#2: Protein/peptide Abz-ALA-THR-THR-PRO-LEU-CYS-GLY-PRO-SER-ARG-ALA-SER-ILE-LEU-SER-GLY-ARG


Mass: 1650.876 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: modified sulfatase sequence motif
Source: (synth.) Thermomonospora curvata DSM 43183 (bacteria)
References: UniProt: D1ADF2*PLUS

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Non-polymers , 4 types, 298 molecules

#3: Chemical ChemComp-CU1 / COPPER (I) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#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.: 294 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.3 Å3/Da / Density % sol: 46.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 10 % PEG 8000, Tris-HCl (0.1 M, pH 7.0) and MgCl2 (0.2 M)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.999997273308 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Dec 17, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999997273308 Å / Relative weight: 1
ReflectionResolution: 1.04→46.48 Å / Num. obs: 155236 / % possible obs: 100 % / Redundancy: 12.1 % / Biso Wilson estimate: 10.36 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.017 / Rrim(I) all: 0.059 / Net I/σ(I): 19.5 / Num. measured all: 1883544 / Scaling rejects: 3387
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.04-1.0610.10.663.575870.9090.2160.695100
5.7-46.4811.40.0410840.9970.0120.04299.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.7.3data scaling
PHASER1.12phasing
PHENIXrefinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5nxl

5nxl


Resolution: 1.04→46.476 Å / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.63
RfactorNum. reflection% reflection
Rfree0.1801 7807 5.03 %
Rwork0.1729 --
obs0.1733 155126 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 37.81 Å2 / Biso mean: 13.3717 Å2 / Biso min: 6.05 Å2
Refinement stepCycle: final / Resolution: 1.04→46.476 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2470 0 4 294 2768
Biso mean--11.65 17.89 -
Num. residues----320
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062580
X-RAY DIFFRACTIONf_angle_d0.9473539
X-RAY DIFFRACTIONf_chiral_restr0.081354
X-RAY DIFFRACTIONf_plane_restr0.008481
X-RAY DIFFRACTIONf_dihedral_angle_d20.177902
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.04-1.05180.24932660.243648405106
1.0518-1.06420.23892520.234248925144
1.0642-1.07720.21052340.22148455079
1.0772-1.09080.21062580.217848645122
1.0908-1.10520.24392690.212848515120
1.1052-1.12030.2242240.205848995123
1.1203-1.13630.21382690.203648385107
1.1363-1.15330.19492920.19848605152
1.1533-1.17130.19962730.195148555128
1.1713-1.19050.19352560.192548915147
1.1905-1.2110.21092340.190648765110
1.211-1.23310.18452720.187448605132
1.2331-1.25680.18552550.182548995154
1.2568-1.28240.20892810.181548565137
1.2824-1.31030.1912350.182549105145
1.3103-1.34080.19172450.176848985143
1.3408-1.37430.1862610.180148885149
1.3743-1.41150.19932640.177649075171
1.4115-1.4530.18752590.176548955154
1.453-1.49990.18622500.1749285178
1.4999-1.55350.1782830.16648585141
1.5535-1.61570.17272910.162948995190
1.6157-1.68930.19532590.160149325191
1.6893-1.77840.18042260.166549585184
1.7784-1.88980.17292280.170849945222
1.8898-2.03570.18642420.164849515193
2.0357-2.24050.1772740.166149655239
2.2405-2.56470.17372790.168749815260
2.5647-3.23120.17522570.179950435300
3.2312-46.52270.15613190.153951865505

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