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- PDB-4x8d: Ergothioneine-biosynthetic sulfoxide synthase EgtB in complex wit... -

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Basic information

Entry
Database: PDB / ID: 4x8d
TitleErgothioneine-biosynthetic sulfoxide synthase EgtB in complex with N,N-dimethyl-histidine and gamma-glutamyl-cysteine
ComponentsSulfoxide synthase EgtB
KeywordsOXIDOREDUCTASE / sulfoxide synthase / 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
GAMMA-GLUTAMYLCYSTEINE / N,N-dimethyl-L-histidine / : / Hercynine oxygenase
Similarity search - Component
Biological speciesMycobacterium thermoresistibile ATCC 19527 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.98 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 / Derived calculations
Category: atom_site / pdbx_audit_support ...atom_site / pdbx_audit_support / pdbx_distant_solvent_atoms / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn / struct_site_gen
Item: _pdbx_audit_support.funding_organization / _pdbx_distant_solvent_atoms.auth_seq_id ..._pdbx_audit_support.funding_organization / _pdbx_distant_solvent_atoms.auth_seq_id / _pdbx_distant_solvent_atoms.neighbor_macromolecule_distance / _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 / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_site_gen.auth_seq_id / _struct_site_gen.symmetry
Revision 2.1Jan 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.ptnr2_symmetry / _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
Revision 2.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)100,87030
Polymers99,1252
Non-polymers1,74528
Water18,2851015
1
A: Sulfoxide synthase EgtB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,55318
Polymers49,5631
Non-polymers99017
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Sulfoxide synthase EgtB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,31712
Polymers49,5631
Non-polymers75411
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)135.292, 135.292, 141.293
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
11A-505-

MG

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
Source method: isolated from a genetically manipulated source
Details: The amino acids GH are left overs from an N-terminal TEV protease cleavage site. The other N- and C-terminal residues are not visible in the electron 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 , 8 types, 1043 molecules

#2: Chemical ChemComp-3GC / GAMMA-GLUTAMYLCYSTEINE


Mass: 250.272 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H14N2O5S
#3: Chemical ChemComp-AVI / N,N-dimethyl-L-histidine


Mass: 183.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H13N3O2
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg
#7: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Cl
#8: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1015 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.26 Å3/Da / Density % sol: 62.29 %
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: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 31, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.98→47.83 Å / Num. obs: 91436 / % possible obs: 100 % / Redundancy: 13.3 % / Biso Wilson estimate: 26.07 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.149 / Rpim(I) all: 0.042 / Net I/σ(I): 13.4 / Num. measured all: 1216498
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
1.98-2.0112.71.2672.15679644560.740.368100
10.84-47.8310.90.0436.871586580.9990.01298.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimless0.3.8data scaling
MOLREPphasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4x8b

4x8b


Resolution: 1.98→47.83 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 15.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1727 4413 4.83 %random selection
Rwork0.1505 86936 --
obs0.1516 91349 99.99 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 98.44 Å2 / Biso mean: 36.7373 Å2 / Biso min: 14.09 Å2
Refinement stepCycle: final / Resolution: 1.98→47.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6710 0 145 1015 7870
Biso mean--31.51 42.99 -
Num. residues----854
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067101
X-RAY DIFFRACTIONf_angle_d1.0459726
X-RAY DIFFRACTIONf_chiral_restr0.041988
X-RAY DIFFRACTIONf_plane_restr0.0051311
X-RAY DIFFRACTIONf_dihedral_angle_d12.8132563
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
1.98-2.00250.25751370.227828292966
2.0025-2.02610.24151350.211128773012
2.0261-2.05080.25081610.199828733034
2.0508-2.07670.21211410.197228532994
2.0767-2.10410.2151380.196428653003
2.1041-2.13290.19021510.183528412992
2.1329-2.16330.19571450.177928643009
2.1633-2.19560.2111480.173728813029
2.1956-2.22990.19621680.171328232991
2.2299-2.26650.17861320.160728733005
2.2665-2.30560.18141240.160429033027
2.3056-2.34750.18341320.155428683000
2.3475-2.39270.17021440.157328763020
2.3927-2.44150.17351540.153728853039
2.4415-2.49460.17761430.148228673010
2.4946-2.55260.19841370.149529123049
2.5526-2.61640.20121370.150928823019
2.6164-2.68720.17261600.153428643024
2.6872-2.76620.1941390.156628983037
2.7662-2.85550.17141640.150328713035
2.8555-2.95760.16181430.145629073050
2.9576-3.0760.19221580.137228853043
3.076-3.21590.14961400.140929303070
3.2159-3.38540.17531400.14629053045
3.3854-3.59750.15231650.139328983063
3.5975-3.87510.14571330.125829623095
3.8751-4.26490.13151230.118529733096
4.2649-4.88150.14061690.1229483117
4.8815-6.14810.17611900.147229703160
6.1481-47.84690.17971620.180531533315
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)
11.79120.50510.552.110.45063.2783-0.0162-0.0575-0.11270.0393-0.03030.18920.1012-0.16730.03590.1551-0.02140.05090.1190.05570.222524.167951.823644.7937
24.1161-0.59982.91874.8911-2.65098.74260.02610.2888-0.4234-0.60670.13410.40240.9713-0.3821-0.20040.2374-0.07690.06140.2105-0.04940.303920.210444.580133.3376
31.21240.6481-0.16761.4541-0.11320.88240.03740.01110.04210.0163-0.02080.0704-0.037-0.0224-0.01770.11560.01750.02790.12010.04370.13835.273.094538.2911
42.5097-0.0816-0.49622.45740.04053.1985-0.0122-0.07730.1885-0.00110.1008-0.50980.01090.5769-0.06530.2266-0.015-0.00030.4348-0.06630.348860.894828.024826.6597
52.18990.1512-0.18921.68830.21151.77450.0120.4015-0.0263-0.35290.0545-0.3099-0.05650.2648-0.06140.3255-0.00120.0640.3249-0.00960.223751.875826.401315.4038
62.4535-0.6618-0.56482.33870.43972.205-0.11930.2242-0.3155-0.1836-0.04340.29960.2694-0.39790.14250.2685-0.0308-0.00520.2289-0.0280.241529.529116.830324.6267
71.5832-0.0061-0.40982.26430.54451.50180.00780.1617-0.0177-0.21260.06480.101-0.013-0.143-0.07230.27120.01880.03150.27620.00810.183231.813325.654224.8557
81.44380.1439-0.06894.16331.95982.77740.0550.6247-0.0747-1.14880.0627-0.2329-0.3683-0.1452-0.13480.62930.02930.0670.4957-0.03480.251538.858325.39815.7731
92.3251-0.4781-0.49572.51410.45462.4125-0.01070.2303-0.3171-0.37520.0147-0.10580.34360.1354-0.00310.35460.01440.04540.264-0.05740.217842.814216.494219.2843
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 7 through 97 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 98 through 125 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 126 through 434 )A0
4X-RAY DIFFRACTION4chain 'B' and (resid 8 through 97 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 98 through 193 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 194 through 245 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 246 through 304 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 305 through 345 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 346 through 433 )B0

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