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- PDB-2q17: Formylglycine Generating Enzyme from Streptomyces coelicolor -

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Basic information

Entry
Database: PDB / ID: 2q17
TitleFormylglycine Generating Enzyme from Streptomyces coelicolor
Componentsformylglycine generating enzyme
KeywordsUNKNOWN FUNCTION / FGE / formylglycine / sulfatase
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-like domain / Sulfatase-modifying factor enzyme superfamily / C-type lectin fold / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Formylglycine-generating enzyme
Similarity search - Component
Biological speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsCarlson, B.L. / Ballister, E.R. / Skordalakes, E. / King, D.S. / Breidenbach, M.A. / Gilmore, S.A. / Berger, J.M. / Bertozzi, C.R.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Function and structure of a prokaryotic formylglycine-generating enzyme.
Authors: Carlson, B.L. / Ballister, E.R. / Skordalakes, E. / King, D.S. / Breidenbach, M.A. / Gilmore, S.A. / Berger, J.M. / Bertozzi, C.R.
History
DepositionMay 23, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Aug 30, 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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)187,61110
Polymers187,4115
Non-polymers2005
Water17,583976
1
A: formylglycine generating enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5222
Polymers37,4821
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: formylglycine generating enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5222
Polymers37,4821
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: formylglycine generating enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5222
Polymers37,4821
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: formylglycine generating enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5222
Polymers37,4821
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: formylglycine generating enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5222
Polymers37,4821
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)142.444, 142.444, 217.067
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein
formylglycine generating enzyme


Mass: 37482.152 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor (bacteria) / Strain: A3(2) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9F3C7
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 976 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.39 Å3/Da / Density % sol: 63.71 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 8
Details: 100 mM Tris, 2.4 M ammonium formate, 0.3% -octylglucoside, 3.2% 2-butanol, pH 8.0, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.1→20 Å / Num. obs: 123276
Reflection shellResolution: 2.1→2.17 Å

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Processing

SoftwareName: REFMAC / Version: 5.2.0019 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Y1E

1y1e


Resolution: 2.1→20 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.936 / SU B: 12.851 / SU ML: 0.14 / Cross valid method: THROUGHOUT / ESU R: 0.563 / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24114 6203 5 %RANDOM
Rwork0.19895 ---
obs0.20106 117425 83.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 41.231 Å2
Baniso -1Baniso -2Baniso -3
1-2.37 Å21.19 Å20 Å2
2--2.37 Å20 Å2
3----3.56 Å2
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11130 0 5 976 12111
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.02111590
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0991.89915856
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.90551453
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.92121.377581
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.894151484
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.61715138
X-RAY DIFFRACTIONr_chiral_restr0.0750.21554
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.029546
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1860.25482
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3010.27775
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.2974
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1190.220
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1240.232
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2160.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.2831.57333
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.422211436
X-RAY DIFFRACTIONr_scbond_it0.79735065
X-RAY DIFFRACTIONr_scangle_it1.1634.54420
X-RAY DIFFRACTIONr_rigid_bond_restr0.518312398
X-RAY DIFFRACTIONr_sphericity_free2.3483981
X-RAY DIFFRACTIONr_sphericity_bonded0.571311195
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 481 -
Rwork0.291 9029 -
obs--88.23 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.8829-0.4571-0.13262.07630.04042.2462-0.1122-0.119-0.11330.29110.01870.11350.2869-0.17520.09350.01710.02880.0292-0.25140.0195-0.119823.804858.886735.419
21.37120.4107-0.84711.4427-0.47073.46770.0129-0.1183-0.02820.02010.0799-0.02950.1661-0.1259-0.0928-0.2383-0.0297-0.0255-0.0666-0.023-0.109213.8881-3.616350.2965
31.67620.1468-0.21822.87010.37793.4612-0.17570.01230.0519-0.34420.1438-0.1244-0.2642-0.18280.0319-0.0929-0.01520.0497-0.2118-0.0266-0.06123.451424.599929.4034
41.5127-0.5185-0.33742.16220.82533.369-0.07570.0540.0470.1706-0.0041-0.01-0.0752-0.13940.0798-0.10410.0608-0.0077-0.17830.0288-0.142660.58632.989856.876
51.9167-0.4321-0.27961.90870.5962.3387-0.1571-0.06270.04240.18540.0922-0.07640.11250.43890.065-0.1040.026-0.0203-0.12670.0464-0.129963.750952.930328.6271
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA18 - 30550 - 337
2X-RAY DIFFRACTION2BB19 - 30651 - 338
3X-RAY DIFFRACTION3CC20 - 30652 - 338
4X-RAY DIFFRACTION4DD20 - 30552 - 337
5X-RAY DIFFRACTION5EE19 - 30751 - 339

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