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

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Basic information

Entry
Database: PDB / ID: 6xtp
TitleCrystal structure reveals non-coordinative binding of O2 to the copper center of the formylglycine-generating enzyme - FGE:Cu:S:O2-1a 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-like domain / 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: 1.8 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)35,0237
Polymers34,7242
Non-polymers2995
Water3,495194
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2380 Å2
ΔGint-44 kcal/mol
Surface area13380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.327, 70.971, 75.640
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 , 5 types, 199 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-OXY / OXYGEN MOLECULE


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


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


Mass: 18.015 Da / Num. of mol.: 194 / 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: 2.22 Å3/Da / Density % sol: 44.49 %
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: 1.8→45.69 Å / Num. obs: 26230 / % possible obs: 89.5 % / Redundancy: 10.4 % / Biso Wilson estimate: 13.64 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.031 / Rrim(I) all: 0.098 / Net I/σ(I): 16.3 / Num. measured all: 272094 / Scaling rejects: 67
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
1.8-1.848.20.5661373016750.9080.2030.6032.399.5
9-45.6910.40.03929822870.9990.0120.04143.799.7

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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: 1.8→45.688 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 33.64
RfactorNum. reflection% reflection
Rfree0.291 1190 4.86 %
Rwork0.2428 --
obs0.2452 24503 83.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 50.92 Å2 / Biso mean: 21.7826 Å2 / Biso min: 8.57 Å2
Refinement stepCycle: final / Resolution: 1.8→45.688 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2418 0 5 194 2617
Biso mean--19.52 23.99 -
Num. residues----313
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072507
X-RAY DIFFRACTIONf_angle_d0.9023434
X-RAY DIFFRACTIONf_chiral_restr0.053344
X-RAY DIFFRACTIONf_plane_restr0.007466
X-RAY DIFFRACTIONf_dihedral_angle_d8.861436
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8-1.8820.44461630.3648316793
1.882-1.98120.66711120.5189227466
1.9812-2.10530.4681460.3756307289
2.1053-2.26790.34041020.2775242696
2.2679-2.49610.33271260.2455314998
2.4961-2.85720.30061620.2383277280
2.8572-3.59960.23151730.2072323592
3.5996-45.6880.21392060.1625321889

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