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- PDB-4x8e: Ergothioneine-biosynthetic sulfoxide synthase EgtB in complex wit... -

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Basic information

Entry
Database: PDB / ID: 4x8e
TitleErgothioneine-biosynthetic sulfoxide synthase EgtB in complex with N,N,N-trimethyl-histidine
ComponentsSulfoxide synthase EgtB
KeywordsOXIDOREDUCTASE / ergothioneine biosynthesis / C-Lectin / DinB / non-heme Fe(II) enzyme
Function / homology
Function and homology information


gamma-glutamyl hercynylcysteine S-oxide synthase / gamma-glutamyl hercynylcysteine sulfoxide synthase activity / monooxygenase activity / iron ion binding
Similarity search - Function
Hercynine oxygenase, Actinobacteria / Ergothioneine biosynthesis protein EgtB / DinB-like domain / DinB superfamily / DinB/YfiT-like putative metalloenzymes / Sulfatase-modifying factor enzyme / Sulfatase-modifying factor enzyme 1 / Sulfatase-modifying factor enzyme superfamily / C-type lectin fold
Similarity search - Domain/homology
N,N,N-trimethyl-histidine / : / Hercynine oxygenase
Similarity search - Component
Biological speciesMycobacterium thermoresistibile ATCC 19527 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å
AuthorsVit, A. / Goncharenko, K.V. / Blankenfeldt, W. / Seebeck, F.P.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation147005 Switzerland
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2015
Title: Structure of the Sulfoxide Synthase EgtB from the Ergothioneine Biosynthetic Pathway.
Authors: Goncharenko, K.V. / Vit, A. / Blankenfeldt, W. / Seebeck, F.P.
History
DepositionDec 10, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 28, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 25, 2015Group: Database references
Revision 2.0Sep 6, 2017Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Derived calculations
Category: atom_site / diffrn_radiation_wavelength ...atom_site / diffrn_radiation_wavelength / pdbx_audit_support / pdbx_distant_solvent_atoms / pdbx_struct_conn_angle / pdbx_validate_close_contact / pdbx_validate_symm_contact / struct_conn / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.occupancy / _pdbx_audit_support.funding_organization / _pdbx_distant_solvent_atoms.auth_seq_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _pdbx_validate_symm_contact.auth_seq_id_1 / _pdbx_validate_symm_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_site_gen.auth_seq_id
Revision 2.1Mar 20, 2019Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / struct_site_gen
Item: _chem_comp.pdbx_synonyms / _struct_site_gen.auth_seq_id / _struct_site_gen.symmetry
Revision 2.2Jan 10, 2024Group: 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _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 / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sulfoxide synthase EgtB
B: Sulfoxide synthase EgtB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,11529
Polymers99,1252
Non-polymers1,99027
Water19,9251106
1
A: Sulfoxide synthase EgtB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,79518
Polymers49,5631
Non-polymers1,23217
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Sulfoxide synthase EgtB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,32011
Polymers49,5631
Non-polymers75810
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)135.241, 135.241, 142.043
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11B-998-

HOH

DetailsThe biological assembly is a monomer. This was confirmed by size exclusion chromatography. The asymmetric unit contains two biological assemblies

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Sulfoxide synthase EgtB


Mass: 49562.574 Da / Num. of mol.: 2 / Fragment: UNP residues 3-446
Source method: isolated from a genetically manipulated source
Details: The first 2 amino acids GH are from a TEV protease cleavage site. Some N- and C-terminal residues are not visible in the elcetron density and have not been built.
Source: (gene. exp.) Mycobacterium thermoresistibile ATCC 19527 (bacteria)
Gene: KEK_08772 / Plasmid: pET19m / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G7CFI3

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Non-polymers , 7 types, 1133 molecules

#2: Chemical ChemComp-AVJ / N,N,N-trimethyl-histidine / Hercynine


Mass: 198.242 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H16N3O2
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1106 / 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: 3.28 Å3/Da / Density % sol: 62.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Tris/HCl pH 7-7.5, 6-12% PEG 8000, 0.2 M magnesium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Apr 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→48.97 Å / Num. obs: 172557 / % possible obs: 100 % / Redundancy: 26.6 % / Biso Wilson estimate: 21.48 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.016 / Net I/σ(I): 32 / Num. measured all: 4581822
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
1.6-1.6326.41.8352.322319584630.7480.363100
8.76-48.9724.40.021134.629919122710.00499.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimless0.1.29data scaling
MOLREPphasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4x8b

4x8b


Resolution: 1.6→48.97 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 15.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1628 8591 4.98 %random selection
Rwork0.1445 163843 --
obs0.1454 172434 99.99 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 102.52 Å2 / Biso mean: 34.1847 Å2 / Biso min: 12.46 Å2
Refinement stepCycle: final / Resolution: 1.6→48.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6717 0 237 1106 8060
Biso mean--42.16 42.25 -
Num. residues----854
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.017135
X-RAY DIFFRACTIONf_angle_d1.3079762
X-RAY DIFFRACTIONf_chiral_restr0.053986
X-RAY DIFFRACTIONf_plane_restr0.0071307
X-RAY DIFFRACTIONf_dihedral_angle_d13.2282609
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.6-1.61820.28482970.237653855682
1.6182-1.63720.24743080.240253705678
1.6372-1.65720.22762830.223253825665
1.6572-1.67820.23382890.207854505739
1.6782-1.70030.23693240.19553315655
1.7003-1.72360.19512910.189453885679
1.7236-1.74820.20323240.176253765700
1.7482-1.77430.18392750.170754095684
1.7743-1.8020.20482880.170754215709
1.802-1.83150.18342700.163854235693
1.8315-1.86310.17412990.160553945693
1.8631-1.8970.18052680.155154325700
1.897-1.93350.18252960.15154225718
1.9335-1.9730.15343030.145453915694
1.973-2.01590.1752520.139754705722
2.0159-2.06280.17142960.138154165712
2.0628-2.11430.16782660.137254755741
2.1143-2.17150.16982770.139654405717
2.1715-2.23540.16143000.132354065706
2.2354-2.30760.15832470.133154985745
2.3076-2.390.16572600.132154925752
2.39-2.48570.15352800.12854775757
2.4857-2.59880.16642680.128754745742
2.5988-2.73590.152760.130655005776
2.7359-2.90720.15393030.134354855788
2.9072-3.13170.152770.132855115788
3.1317-3.44680.16452760.141555555831
3.4468-3.94530.14252750.136855835858
3.9453-4.96990.13832850.129556395924
4.9699-48.99610.15893380.163958486186
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)
11.620.9835-0.02042.50691.83254.6979-0.09030.0312-0.2379-0.13850.0152-0.10770.0750.13920.06190.17080.00330.04690.12910.04080.226732.293351.280241.8552
21.73050.4862-0.11982.4838-0.05213.1502-0.13130.0845-0.1115-0.14670.09450.41130.1924-0.28570.04160.1497-0.04940.01930.15680.04110.258419.006549.825643.1398
31.14640.4502-0.15161.6203-0.29690.92530.02590.00590.00150.0148-0.02030.0554-0.02210.0006-0.00620.10010.00090.01250.11310.02870.109434.834173.247938.3647
42.1626-0.3426-0.55252.58650.35891.96110.08720.04670.2915-0.15550.1402-0.5552-0.04630.561-0.20370.2463-0.03720.02960.4954-0.05520.329260.839129.025624.2307
52.6013-0.02210.06111.94650.31151.88980.06830.04950.1783-0.08440.117-0.4628-0.10470.456-0.17690.2979-0.03620.05310.372-0.03050.274656.266828.825423.2774
62.0137-0.3109-0.7961.83420.6292.03250.01190.296-0.1277-0.34620.02950.01760.0322-0.0268-0.03370.31320.0111-0.00510.2577-0.00140.157837.101219.661319.1315
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 7 through 44 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 45 through 125 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 126 through 434 )A0
4X-RAY DIFFRACTION4chain 'B' and (resid 8 through 73 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 74 through 171 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 172 through 433 )B0

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