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- PDB-6xts: Crystal structure reveals non-coordinative binding of O2 to the c... -

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Basic information

Entry
Database: PDB / ID: 6xts
TitleCrystal structure reveals non-coordinative binding of O2 to the copper center of the formylglycine-generating enzyme - FGE:Cu:S:O2-1d complex
Components
  • ABZ-ALA-THR-THR-PRO-LEU-CYS-GLY-PRO-SER-ARG-ALA-SER-ILE-LEU-SER-GLY
  • Formylglycine-generating enzyme
KeywordsTRANSFERASE / Formylglycine-generating enzyme / complex / substrate analog / copper
Function / homology
Function and homology information


formylglycine-generating enzyme / formylglycine-generating oxidase activity / protein oxidation / cuprous ion binding / post-translational protein modification / metal ion binding
Similarity search - Function
: / 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
Similarity search - Domain/homology
COPPER (I) ION / OXYGEN MOLECULE / ISATOIC ANHYDRIDE / Formylglycine-generating enzyme / Sulfatase
Similarity search - Component
Biological speciesThermomonospora curvata (bacteria)
Thermomonospora curvata DSM 43183 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsLeisinger, F. / Seebeck, F.P.
Funding support Switzerland, European Union, 2items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
European Research Council (ERC)ERC-2013- StG 336559European Union
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2020
Title: Non-Coordinative Binding of O2 at the Active Center of a Copper-Dependent Enzyme
Authors: Leisinger, F. / Miarzlou, D.A. / Seebeck, F.P.
History
DepositionJan 16, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 27, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 11, 2021Group: Advisory / Database references
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 24, 2024Group: 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
A: Formylglycine-generating enzyme
C: ABZ-ALA-THR-THR-PRO-LEU-CYS-GLY-PRO-SER-ARG-ALA-SER-ILE-LEU-SER-GLY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0598
Polymers34,7242
Non-polymers3346
Water6,936385
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2440 Å2
ΔGint-41 kcal/mol
Surface area13630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.104, 72.222, 76.886
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)
Gene: Tcur_4811 / Plasmid: pET19 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS
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


Mass: 1387.625 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 , 6 types, 391 molecules

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


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#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: Chemical ChemComp-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O2
#7: Chemical ChemComp-SOA / ISATOIC ANHYDRIDE


Mass: 123.152 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H9NO
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 385 / 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: 2.32 Å3/Da / Density % sol: 47.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 7-12 % PEG 8000, 0.2-0.3 M MgCl2, Tris-HCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.0006777109999 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Oct 5, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0006777109999 Å / Relative weight: 1
ReflectionResolution: 1.2→46.36 Å / Num. obs: 99101 / % possible obs: 97.5 % / Redundancy: 12.5 % / Biso Wilson estimate: 10.76 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.015 / Rrim(I) all: 0.054 / Net I/σ(I): 27 / Num. measured all: 1237436 / Scaling rejects: 19
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.2-1.2211.90.7835927849860.9330.2350.8183.499.9
6.57-46.3610.80.025779872210.0080.02692.899.8

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.4data scaling
PHENIX1.17.1refinement
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6S07

6s07


Resolution: 1.2→46.356 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 22.04
RfactorNum. reflection% reflection
Rfree0.2159 4833 4.93 %
Rwork0.1998 --
obs0.2006 98094 96.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 42.75 Å2 / Biso mean: 14.3945 Å2 / Biso min: 6.25 Å2
Refinement stepCycle: final / Resolution: 1.2→46.356 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2460 0 7 385 2852
Biso mean--13.96 21.81 -
Num. residues----318
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092583
X-RAY DIFFRACTIONf_angle_d1.1243542
X-RAY DIFFRACTIONf_chiral_restr0.086353
X-RAY DIFFRACTIONf_plane_restr0.01481
X-RAY DIFFRACTIONf_dihedral_angle_d8.7521430
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.2-1.21360.34581890.3068310398
1.2136-1.22790.43641630.4207312699
1.2279-1.24290.33391630.3328307596
1.2429-1.25860.29261530.29063172100
1.2586-1.27520.36181680.33133165100
1.2752-1.29270.36911360.3477306095
1.2927-1.31110.44581500.425295993
1.3111-1.33070.21861730.22143204100
1.3307-1.35150.22781530.20263223100
1.3515-1.37370.28851420.25043185100
1.3737-1.39730.21731570.2173203100
1.3973-1.42280.22251700.20213203100
1.4228-1.45010.25671550.21633199100
1.4501-1.47970.24641560.2242316099
1.4797-1.51190.22951500.2114315398
1.5119-1.54710.21391680.20663188100
1.5471-1.58580.18811600.17643195100
1.5858-1.62860.17591900.1793209100
1.6286-1.67660.17581670.17353195100
1.6766-1.73070.20011720.17643202100
1.7307-1.79250.18111670.18683212100
1.7925-1.86430.22721650.19423209100
1.8643-1.94920.24931890.2451309596
1.9492-2.05190.19891800.1821318399
2.0519-2.18050.21091730.183234100
2.1805-2.34880.17541020.175201962
2.3488-2.58520.21611750.18713260100
2.5852-2.95920.22121310.1882266281
2.9592-3.72810.17521310.1748288787
3.7281-46.3560.16831850.1486332196

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