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- PDB-4x8b: Ergothioneine-biosynthetic sulfoxide synthase EgtB, apo form -

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Basic information

Entry
Database: PDB / ID: 4x8b
TitleErgothioneine-biosynthetic sulfoxide synthase EgtB, apo form
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
: / Hercynine oxygenase
Similarity search - Component
Biological speciesMycobacterium thermoresistibile ATCC 19527 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsVit, A. / Goncharenko, K.V. / Blankenfeldt, W. / Seebeck, F.P.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation1147005 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 / Refinement description
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 / software / 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 / _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 / _software.name / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_site_gen.auth_seq_id

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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)100,35720
Polymers99,1252
Non-polymers1,23218
Water21,6721203
1
A: Sulfoxide synthase EgtB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,17910
Polymers49,5631
Non-polymers6169
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Sulfoxide synthase EgtB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,17910
Polymers49,5631
Non-polymers6169
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)134.780, 134.780, 141.204
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
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 N-terminal residues GH are left overs from an N-terminal TEV protease cleavage site. Some other N- and C-terminal residues were 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 , 6 types, 1221 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-FE / FE (III) ION


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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1203 / 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: 3.23 Å3/Da / Density % sol: 61.97 %
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

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSLS X06DA12.066
SYNCHROTRONSLS X06DA21
Detector
TypeIDDetectorDate
DECTRIS PILATUS 2M-F1PIXELFeb 14, 2014
DECTRIS PILATUS 2M-F2PIXELFeb 14, 2014
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
12.0661
211
ReflectionRedundancy: 43.6 % / Number: 2559724 / Rmerge(I) obs: 0.059 / D res high: 2.27 Å / D res low: 48.83 Å / Num. obs: 58661 / % possible obs: 96.4
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)IDRmerge(I) obsRedundancy
2.272.3310.29520.9
9.948.8310.02949.4
ReflectionResolution: 1.7→48.75 Å / Num. obs: 142371 / % possible obs: 100 % / Redundancy: 26.6 % / Biso Wilson estimate: 19.98 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.118 / Rpim(I) all: 0.023 / Net I/σ(I): 24.6 / Num. measured all: 3781286 / Scaling rejects: 4
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
1.7-1.7327.51.5782.719159169660.7850.306100
9.31-48.7523.50.02887.124060102210.00699.4

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
Aimless0.2.17data scaling
SHELXDEphasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
ARPmodel building
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.7→48.748 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 13.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1569 7009 4.93 %random selection
Rwork0.1377 135254 --
obs0.1387 142263 99.99 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 92.93 Å2 / Biso mean: 28.9402 Å2 / Biso min: 10.4 Å2
Refinement stepCycle: final / Resolution: 1.7→48.748 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6708 0 162 1203 8073
Biso mean--41.01 40.13 -
Num. residues----854
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097064
X-RAY DIFFRACTIONf_angle_d1.2149659
X-RAY DIFFRACTIONf_chiral_restr0.046979
X-RAY DIFFRACTIONf_plane_restr0.0071293
X-RAY DIFFRACTIONf_dihedral_angle_d13.2882597
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
1.7-1.71930.21792530.20144114664
1.7193-1.73960.22792650.197544154680
1.7396-1.76080.21042260.187244594685
1.7608-1.78310.19992340.184644524686
1.7831-1.80650.18352460.179644454691
1.8065-1.83130.2062100.169544884698
1.8313-1.85740.18782450.170844294674
1.8574-1.88520.19772270.164544794706
1.8852-1.91460.18362440.156744514695
1.9146-1.9460.16662560.147844674723
1.946-1.97960.14992220.144344534675
1.9796-2.01560.17072090.138545104719
2.0156-2.05430.16632500.135844514701
2.0543-2.09630.1682130.134144764689
2.0963-2.14180.15482400.133145064746
2.1418-2.19170.16672220.129444494671
2.1917-2.24650.14282400.129545104750
2.2465-2.30720.14871960.125844954691
2.3072-2.37510.16982210.126545254746
2.3751-2.45180.13642360.125544974733
2.4518-2.53940.15072170.122545344751
2.5394-2.64110.15022200.129445324752
2.6411-2.76120.13882350.128645084743
2.7612-2.90680.1452480.133744964744
2.9068-3.08890.16762350.130445434778
3.0889-3.32730.16432180.132545814799
3.3273-3.66210.14332510.132245674818
3.6621-4.19170.12861920.118646434835
4.1917-5.28020.12792500.121446574907
5.2802-48.76790.17752880.172848255113
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)
11.37470.3338-0.02181.85590.30023.2618-0.03150.0234-0.1639-0.0874-0.02680.11370.1299-0.13480.04610.1087-0.010.02660.07740.02380.17823.070649.96742.2529
20.90690.3456-0.15391.2403-0.21510.72480.02390.01260.00350.0054-0.0469-0.0695-0.0380.10790.02450.0904-0.0040.01220.10780.02570.112237.688373.04137.8866
31.39540.34090.37871.8122-0.02861.17970.0607-0.09310.03880.0694-0.02630.2627-0.0034-0.1758-0.04370.0939-0.00160.02210.10560.02770.137525.995271.976839.2651
42.11780.1201-0.01351.77270.05032.28610.01330.06360.044-0.0690.0253-0.41030.030.499-0.04450.15190.00430.01240.2639-0.01330.227860.915227.8923.7514
51.1734-0.2107-0.22471.71790.4571.53030.03630.1954-0.0617-0.2682-0.00980.0641-0.028-0.1524-0.02050.1820.0195-0.010.19030.0010.127733.837722.778418.5229
62.6851-0.4373-0.91292.28740.46731.993-0.0368-0.0045-0.2398-0.11660.0638-0.11250.27210.1446-0.02770.21070.02340.00250.1564-0.02510.136542.665316.341719.4301
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 7 through 125 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 126 through 365 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 366 through 434 )A0
4X-RAY DIFFRACTION4chain 'B' and (resid 8 through 148 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 149 through 345 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 346 through 433 )B0

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