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- PDB-6qkj: EgtB from Chloracidobacterium thermophilum, a type II sulfoxide s... -

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Basic information

Entry
Database: PDB / ID: 6qkj
TitleEgtB from Chloracidobacterium thermophilum, a type II sulfoxide synthase in complex with N,N,N-trimethyl-histidine
ComponentsUncharacterized protein
KeywordsOXIDOREDUCTASE / ERGOTHIONEINE BIOSYNTHESIS / C-LECTIN / DINB / NON-HEME FE(II) ENZYME / SULFOXIDE SYNTHASE
Function / homology
Function and homology information


ergothioneine biosynthetic process / oxidoreductase activity / metal ion binding
Similarity search - Function
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 / : / IMIDAZOLE / Ergothioneine biosynthesis protein EgtB
Similarity search - Component
Biological speciesChloracidobacterium thermophilum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsStampfli, A.R. / Badri, B.N. / Schirmer, T. / Seebeck, F.P.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
European Research CouncilERC-2013- StG 336559 Switzerland
CitationJournal: J.Am.Chem.Soc. / Year: 2019
Title: An Alternative Active Site Architecture for O2Activation in the Ergothioneine Biosynthetic EgtB from Chloracidobacterium thermophilum.
Authors: Stampfli, A.R. / Goncharenko, K.V. / Meury, M. / Dubey, B.N. / Schirmer, T. / Seebeck, F.P.
History
DepositionJan 29, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 27, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2May 15, 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 / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,78114
Polymers98,8812
Non-polymers90012
Water4,954275
1
A: Uncharacterized protein
B: Uncharacterized protein
hetero molecules

A: Uncharacterized protein
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)199,56228
Polymers197,7624
Non-polymers1,80024
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area12930 Å2
ΔGint-261 kcal/mol
Surface area62130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.143, 201.288, 108.332
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: MET / End label comp-ID: MET / Refine code: _ / Auth seq-ID: 17 - 433 / Label seq-ID: 20 - 436

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Uncharacterized protein


Mass: 49440.457 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chloracidobacterium thermophilum (strain B) (bacteria)
Gene: Cabther_A1318 / Plasmid: pET19 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: G2LET6

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Non-polymers , 5 types, 287 molecules

#2: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-AVJ / N,N,N-trimethyl-histidine / Hercynine


Mass: 198.242 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H16N3O2
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 275 / 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: 2.98 Å3/Da / Density % sol: 58.79 %
Crystal growTemperature: 303.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.09 M NPS (0.3M Sodium nitrate, 0.3 Sodium phosphate dibasic, 0.3M Ammonium sulfate), 0.1 Buffer system 1 (0.1 M Buffer system 1 Imidazole: MES monohydrate (acid)), pH 6.5, 50 % precipitant ...Details: 0.09 M NPS (0.3M Sodium nitrate, 0.3 Sodium phosphate dibasic, 0.3M Ammonium sulfate), 0.1 Buffer system 1 (0.1 M Buffer system 1 Imidazole: MES monohydrate (acid)), pH 6.5, 50 % precipitant mix 2 (40% v/v Ethylene glycol: 20 % w/v PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.033 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Nov 28, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.2→29.68 Å / Num. obs: 60190 / % possible obs: 99.92 % / Redundancy: 13 % / Biso Wilson estimate: 31.24 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.2683 / Rpim(I) all: 0.07704 / Rrim(I) all: 0.2793 / Net I/σ(I): 11.23
Reflection shellResolution: 2.2→2.279 Å / Redundancy: 11.5 % / Rmerge(I) obs: 2.007 / Mean I/σ(I) obs: 1.46 / Num. unique obs: 5960 / CC1/2: 0.571 / Rpim(I) all: 0.6147 / Rrim(I) all: 2.1 / % possible all: 99.92

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation7.55 Å94.92 Å
Translation7.55 Å94.92 Å

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0232refinement
XDSdata reduction
Aimlessdata scaling
PHASER2.5.6phasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→29.68 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.926 / SU B: 13.588 / SU ML: 0.143 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.213 / ESU R Free: 0.186
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2375 2927 4.9 %RANDOM
Rwork0.1946 ---
obs0.1966 57265 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 120.79 Å2 / Biso mean: 33.445 Å2 / Biso min: 19.05 Å2
Baniso -1Baniso -2Baniso -3
1-1.21 Å20 Å20 Å2
2---0.27 Å20 Å2
3----0.94 Å2
Refinement stepCycle: final / Resolution: 2.2→29.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6634 0 46 275 6955
Biso mean--32.97 30.93 -
Num. residues----824
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0136954
X-RAY DIFFRACTIONr_bond_other_d0.0020.0176125
X-RAY DIFFRACTIONr_angle_refined_deg1.6251.6579516
X-RAY DIFFRACTIONr_angle_other_deg1.3921.57514113
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3815832
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.63619.831414
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.04515969
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6931569
X-RAY DIFFRACTIONr_chiral_restr0.0790.2840
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.027995
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021730
Refine LS restraints NCS

Ens-ID: 1 / Number: 14033 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.05 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.2→2.257 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 209 -
Rwork0.311 4186 -
all-4395 -
obs--99.86 %
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)
10.01920.02070.05220.11620.03310.24930.00010.01290.00470.02270.0059-0.00480.020.0325-0.0060.00990.0034-0.00620.03030.00290.00628.72720.9412-9.8416
20.1177-0.00980.10950.1882-0.11780.2066-0.0164-0.01030.02310.0494-0.0129-0.0072-0.0367-0.01890.02930.0182-0.0031-0.00930.0095-0.00650.0164.08967.1312-8.5327
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 434
2X-RAY DIFFRACTION2B17 - 434

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