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

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Basic information

Entry
Database: PDB / ID: 6xtn
TitleCrystal structure reveals non-coordinative binding of O2 to the copper center of the formylglycine-generating enzyme - FGE:Ag:S:NO 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


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
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
SILVER ION / NITRIC OXIDE / 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: 1.4 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)35,3079
Polymers34,8692
Non-polymers4397
Water5,567309
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2560 Å2
ΔGint-34 kcal/mol
Surface area13890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.299, 71.898, 76.919
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: 1531.755 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 , 7 types, 316 molecules

#3: Chemical ChemComp-AG / SILVER ION / Silver


Mass: 107.868 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ag
#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 / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-NO / NITRIC OXIDE / Nitrogen monoxide / Nitric oxide


Mass: 30.006 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO
#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#8: Chemical ChemComp-SOA / ISATOIC ANHYDRIDE / Isatoic anhydride


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


Mass: 18.015 Da / Num. of mol.: 309 / 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: 2.31 Å3/Da / Density % sol: 46.79 % / Mosaicity: 0.15 °
Crystal growTemperature: 303.15 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: 0.98298 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 5, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98298 Å / Relative weight: 1
ReflectionResolution: 1.4→46.462 Å / Num. obs: 64363 / % possible obs: 100 % / Redundancy: 13.1 % / Biso Wilson estimate: 13.83 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.016 / Rrim(I) all: 0.058 / Net I/σ(I): 25.8
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
1.4-1.4213.60.6574419232450.930.1840.6824.499.9
7.54-46.4611.60.027568649210.0080.02965.799.7

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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: 1.4→46.462 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.22
RfactorNum. reflection% reflection
Rfree0.1956 3190 4.96 %
Rwork0.1692 --
obs0.1705 64288 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 47.04 Å2 / Biso mean: 16.2032 Å2 / Biso min: 8.27 Å2
Refinement stepCycle: final / Resolution: 1.4→46.462 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2470 0 12 309 2791
Biso mean--20.03 22.55 -
Num. residues----320
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072588
X-RAY DIFFRACTIONf_angle_d1.0153545
X-RAY DIFFRACTIONf_chiral_restr0.085353
X-RAY DIFFRACTIONf_plane_restr0.008482
X-RAY DIFFRACTIONf_dihedral_angle_d21.397907
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.4-1.42090.26971510.21322614
1.4209-1.44310.25221340.20562628
1.4431-1.46680.22561370.192620
1.4668-1.49210.21491260.18012626
1.4921-1.51920.18981250.17172626
1.5192-1.54840.20211250.17062630
1.5484-1.580.19921490.16352605
1.58-1.61440.18831600.15992615
1.6144-1.65190.16451230.15992642
1.6519-1.69320.17721490.16152637
1.6932-1.7390.19611400.16292598
1.739-1.79020.17751660.16912660
1.7902-1.8480.19841540.17032616
1.848-1.9140.21031380.17162633
1.914-1.99070.18321310.16942657
1.9907-2.08130.19671290.16992676
2.0813-2.1910.20281330.17182671
2.191-2.32830.19181240.1722678
2.3283-2.5080.21241540.18112667
2.508-2.76040.2041480.18462679
2.7604-3.15980.21171510.19252668
3.1598-3.98060.17931180.15992759
3.9806-46.4620.1741250.14122893

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