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

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Basic information

Entry
Database: PDB / ID: 6xtr
TitleCrystal structure reveals non-coordinative binding of O2 to the copper center of the formylglycine-generating enzyme - FGE:Cu:S:O2-1c 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: 1.2 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)35,2389
Polymers34,8692
Non-polymers3707
Water6,125340
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2530 Å2
ΔGint-44 kcal/mol
Surface area13890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.970, 71.674, 76.435
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 , 6 types, 347 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.: 2 / 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.: 340 / 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: 2.28 Å3/Da / Density % sol: 45.98 %
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→46.19 Å / Num. obs: 100095 / % possible obs: 100 % / Redundancy: 12.8 % / Biso Wilson estimate: 13.4 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.047 / Rpim(I) all: 0.014 / Rrim(I) all: 0.049 / Net I/σ(I): 25.3 / Num. measured all: 1277049 / Scaling rejects: 31
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
1.2-1.2212.30.8356019748820.8570.2470.8713.1100
6.57-46.1911.20.02679287080.9990.0080.0278199.8

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.4data scaling
PHENIX1.12_2829refinement
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6S07

6s07


Resolution: 1.2→46.189 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 21.11
RfactorNum. reflection% reflection
Rfree0.2059 4906 4.91 %
Rwork0.1888 --
obs0.1896 100004 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 54.89 Å2 / Biso mean: 17.7215 Å2 / Biso min: 8.83 Å2
Refinement stepCycle: final / Resolution: 1.2→46.189 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2470 0 8 340 2818
Biso mean--20.2 24.83 -
Num. residues----320
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072588
X-RAY DIFFRACTIONf_angle_d0.9833550
X-RAY DIFFRACTIONf_chiral_restr0.079355
X-RAY DIFFRACTIONf_plane_restr0.008483
X-RAY DIFFRACTIONf_dihedral_angle_d8.7631434
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.2-1.21360.28871580.26733151
1.2136-1.22790.29631810.26353085
1.2279-1.24290.26171540.26113125
1.2429-1.25860.2931720.25363176
1.2586-1.27520.30081440.25143119
1.2752-1.29270.26551560.24863151
1.2927-1.31110.27511570.24663151
1.3111-1.33070.27711780.24363106
1.3307-1.35150.24791330.23063180
1.3515-1.37370.2551430.2343156
1.3737-1.39740.26161600.22893132
1.3974-1.42280.25951660.22693130
1.4228-1.45010.2481530.2173176
1.4501-1.47970.23491570.21993153
1.4797-1.51190.23691500.21263160
1.5119-1.54710.22411620.20983144
1.5471-1.58580.22211630.2013154
1.5858-1.62870.20761840.19923145
1.6287-1.67660.18261660.19243154
1.6766-1.73070.21941720.19923147
1.7307-1.79260.18291610.19843180
1.7926-1.86430.24431720.19343169
1.8643-1.94920.22251920.19373144
1.9492-2.05190.19941770.18083192
2.0519-2.18050.1941680.18663192
2.1805-2.34890.18521640.17663180
2.3489-2.58520.20781680.18893206
2.5852-2.95920.20381700.18893235
2.9592-3.72810.19471410.16933297
3.7281-46.1890.16091840.15063408

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