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- PDB-6muj: Formylglycine generating enzyme bound to copper -

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Basic information

Entry
Database: PDB / ID: 6muj
TitleFormylglycine generating enzyme bound to copper
ComponentsFormylglycine-generating enzyme
KeywordsMETAL BINDING PROTEIN / formylglycine / copper oxidase / metalloenzyme
Function / homology
Function and homology information


formylglycine-generating enzyme / formylglycine-generating oxidase activity / protein oxidation / cupric ion binding / post-translational protein modification / calcium 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 / C-type lectin fold / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
COPPER (II) ION / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / FORMIC ACID / GLYCINE / IMIDAZOLE / Formylglycine-generating enzyme
Similarity search - Component
Biological speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.249 Å
AuthorsLafrance-Vanasse, J. / Appel, M.J. / Tsai, C.-L. / Bertozzi, C. / Tainer, J.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R35CA22043 United States
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2019
Title: Formylglycine-generating enzyme binds substrate directly at a mononuclear Cu(I) center to initiate O2activation.
Authors: Appel, M.J. / Meier, K.K. / Lafrance-Vanasse, J. / Lim, H. / Tsai, C.L. / Hedman, B. / Hodgson, K.O. / Tainer, J.A. / Solomon, E.I. / Bertozzi, C.R.
History
DepositionOct 23, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 27, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
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.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Mar 27, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Formylglycine-generating enzyme
B: Formylglycine-generating enzyme
C: Formylglycine-generating enzyme
D: Formylglycine-generating enzyme
E: Formylglycine-generating enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,78441
Polymers171,3935
Non-polymers2,39136
Water11,764653
1
A: Formylglycine-generating enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6427
Polymers34,2791
Non-polymers3636
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Formylglycine-generating enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5786
Polymers34,2791
Non-polymers3005
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Formylglycine-generating enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,89510
Polymers34,2791
Non-polymers6179
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Formylglycine-generating enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,02711
Polymers34,2791
Non-polymers74810
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Formylglycine-generating enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6427
Polymers34,2791
Non-polymers3636
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)140.008, 140.008, 217.508
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11C-681-

HOH

21C-742-

HOH

31C-754-

HOH

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Components

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Protein , 1 types, 5 molecules ABCDE

#1: Protein
Formylglycine-generating enzyme / / sc-FGE


Mass: 34278.598 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor (bacteria) / Strain: ATCC BAA-471 / A3(2) / M145 / Gene: SCO7548 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9F3C7, formylglycine-generating enzyme

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Non-polymers , 8 types, 689 molecules

#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: Cu
#4: Chemical
ChemComp-IMD / IMIDAZOLE / Imidazole


Mass: 69.085 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H5N2
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#7: Chemical ChemComp-GLY / GLYCINE / Glycine


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H5NO2
#8: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL / Dithiothreitol


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 653 / 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: 3.84 Å3/Da / Density % sol: 67.99 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Crystals were grown by hanging-drop vapor diffusion at 23C for one week using a 2uL:2uL mixture of protein solution (8 mg/ml in 50 mM Tris 7.5, 0.5 M NaCl, 10% glycerol, 1 mM DTT) and ...Details: Crystals were grown by hanging-drop vapor diffusion at 23C for one week using a 2uL:2uL mixture of protein solution (8 mg/ml in 50 mM Tris 7.5, 0.5 M NaCl, 10% glycerol, 1 mM DTT) and precipitant buffer (100 mM Tris 8.0, 3.2 M ammonium formate, 0.3% octyl-beta-glucoside (w/v), 3.2% 2-butanol (v/v)) in Easy-Xtal trays. Crystals were soaked in 1mM DTT (in precipitant buffer) for 15 minutes, then soaked in CuCl2 (in precipitant buffer) for 30 minutes, and finally, backsoaked and cryoprotected in 20% glycerol (in precipitant buffer).

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 1.115834 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.115834 Å / Relative weight: 1
ReflectionResolution: 2.249→38.738 Å / % possible obs: 93.95 % / Redundancy: 10.8 % / Net I/σ(I): 12.72
Reflection shellResolution: 2.249→2.33 Å / Redundancy: 8.8 % / Mean I/σ(I) obs: 0.65 / Num. unique obs: 11546 / % possible all: 83.18

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2Q17

2q17


Resolution: 2.249→38.738 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 30.73
RfactorNum. reflection% reflection
Rfree0.2457 3296 1.72 %
Rwork0.2024 --
obs0.2031 191204 84.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 118.97 Å2 / Biso mean: 48.556 Å2 / Biso min: 23.9 Å2
Refinement stepCycle: final / Resolution: 2.249→38.738 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11247 0 84 653 11984
Biso mean--65.1 47.19 -
Num. residues----1456
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00811704
X-RAY DIFFRACTIONf_angle_d0.93215978
X-RAY DIFFRACTIONf_chiral_restr0.0511567
X-RAY DIFFRACTIONf_plane_restr0.0062145
X-RAY DIFFRACTIONf_dihedral_angle_d8.377090
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 24

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2493-2.28150.5085860.47225347543358
2.2815-2.31550.46021010.41736047614865
2.3155-2.35170.44111050.39356236634167
2.3517-2.39030.38891180.37456309642768
2.3903-2.43150.35831280.3686473660170
2.4315-2.47570.45081210.35456505662670
2.4757-2.52330.35261300.33416715684572
2.5233-2.57480.3571230.30897030715376
2.5748-2.63070.30411270.31187230735778
2.6307-2.69190.42141300.29897352748279
2.6919-2.75920.29551340.28597504763881
2.7592-2.83380.30731370.27057890802785
2.8338-2.91720.3191430.27178199834288
2.9172-3.01130.28381470.25598367851490
3.0113-3.11890.30221520.24528555870792
3.1189-3.24370.25611520.22968798895095
3.2437-3.39120.27411600.21518949910997
3.3912-3.56990.25271530.19429097925098
3.5699-3.79340.20151560.16419150930699
3.7934-4.0860.16171540.14449208936299
4.086-4.49660.17641580.13079207936599
4.4966-5.1460.20881560.134692769432100
5.146-6.47850.211590.143192399398100
6.4785-38.74410.16871660.14949225939199

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