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- PDB-6s7q: Crystal structure of ergothioneine degrading enzyme Ergothionase ... -

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Basic information

Entry
Database: PDB / ID: 6s7q
TitleCrystal structure of ergothioneine degrading enzyme Ergothionase from Treponema denticola in complex with desmethyl-ergothioneine sulfonic acid
Componentsergothionase
KeywordsLYASE / ergothioneine degrading enzyme / TdETL / trimethlyammonium lyase / ergothioneine
Function / homologyammonia-lyase activity / Aromatic amino acid lyase / Aromatic amino acid lyase / Fumarase/histidase, N-terminal / L-Aspartase-like / Chem-KZ5 / Histidine ammonia-lyase
Function and homology information
Biological speciesTreponema denticola (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsLeisinger, F. / Seebeck, F.P.
Funding support Switzerland, 2items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
European Research CouncilERC-2013- StG 336559 Switzerland
CitationJournal: Chemistry / Year: 2019
Title: Structure and Mechanism of Ergothionase from Treponema denticola.
Authors: Maurer, A. / Leisinger, F. / Lim, D. / Seebeck, F.P.
History
DepositionJul 5, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 17, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: ergothionase
B: ergothionase
C: ergothionase
D: ergothionase
E: ergothionase
F: ergothionase
G: ergothionase
H: ergothionase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)447,68016
Polymers445,5738
Non-polymers2,1068
Water3,585199
1
A: ergothionase
B: ergothionase
C: ergothionase
D: ergothionase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)223,8408
Polymers222,7874
Non-polymers1,0534
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28040 Å2
ΔGint-143 kcal/mol
Surface area55160 Å2
MethodPISA
2
E: ergothionase
H: ergothionase
hetero molecules

F: ergothionase
G: ergothionase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)223,8408
Polymers222,7874
Non-polymers1,0534
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_545x,y-1,z1
Buried area28580 Å2
ΔGint-149 kcal/mol
Surface area55310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.758, 76.937, 174.842
Angle α, β, γ (deg.)88.560, 81.410, 79.790
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain C
41chain D
51chain E
61chain F
71chain G
81chain H

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: ILE / End label comp-ID: ILE / Auth seq-ID: 2 - 498 / Label seq-ID: 1 - 497

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA
2chain BBB
3chain CCC
4chain DDD
5chain EEE
6chain FFF
7chain GGG
8chain HHH

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Components

#1: Protein
ergothionase


Mass: 55696.668 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Treponema denticola (bacteria) / Gene: HMPREF9733_00339 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: M2BPW8
#2: Chemical
ChemComp-KZ5 / (2~{S})-2-(dimethylamino)-3-(2-sulfo-1~{H}-imidazol-4-yl)propanoic acid


Mass: 263.271 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C8H13N3O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 199 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.26 Å3/Da / Density % sol: 45.46 %
Crystal growTemperature: 293.5 K / Method: vapor diffusion, sitting drop / Details: PEG4000, PEG200, CaCl2, Tris-HCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.979399 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jun 23, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979399 Å / Relative weight: 1
ReflectionResolution: 2.7→49.05 Å / Num. obs: 105530 / % possible obs: 98.7 % / Redundancy: 3.5 % / Biso Wilson estimate: 23.93 Å2 / CC1/2: 0.988 / Rmerge(I) obs: 0.124 / Rpim(I) all: 0.078 / Rrim(I) all: 0.147 / Net I/σ(I): 5.8 / Num. measured all: 365688 / Scaling rejects: 8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.7-2.753.50.3791853053210.8760.2360.4482.398.2
14.79-49.053.30.04820936250.980.0330.05913.696.2

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHENIXrefinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1gkm

1gkm


Resolution: 2.7→49.05 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 28.91
RfactorNum. reflection% reflection
Rfree0.2605 5182 4.91 %
Rwork0.2257 --
obs0.2274 105499 98.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 73.78 Å2 / Biso mean: 25.367 Å2 / Biso min: 6.75 Å2
Refinement stepCycle: final / Resolution: 2.7→49.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms31216 0 240 199 31655
Biso mean--29.85 18.48 -
Num. residues----3976
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00231907
X-RAY DIFFRACTIONf_angle_d0.55343064
X-RAY DIFFRACTIONf_chiral_restr0.0384840
X-RAY DIFFRACTIONf_plane_restr0.0035616
X-RAY DIFFRACTIONf_dihedral_angle_d16.15419480
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A19635X-RAY DIFFRACTION10.541TORSIONAL
12B19635X-RAY DIFFRACTION10.541TORSIONAL
13C19635X-RAY DIFFRACTION10.541TORSIONAL
14D19635X-RAY DIFFRACTION10.541TORSIONAL
15E19635X-RAY DIFFRACTION10.541TORSIONAL
16F19635X-RAY DIFFRACTION10.541TORSIONAL
17G19635X-RAY DIFFRACTION10.541TORSIONAL
18H19635X-RAY DIFFRACTION10.541TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.7-2.73070.35481550.28340098
2.7307-2.76280.28951560.2791328098
2.7628-2.79650.33391640.2781332798
2.7965-2.83190.35531630.2709337898
2.8319-2.86910.30231630.2696335698
2.8691-2.90840.32981850.2735327998
2.9084-2.950.32541730.2664340699
2.95-2.9940.33291920.2667323198
2.994-3.04080.30562090.2773328298
3.0408-3.09060.33471850.2744337299
3.0906-3.14390.27241710.2615329098
3.1439-3.20110.31211890.2638340799
3.2011-3.26260.31031860.2634327199
3.2626-3.32920.29431590.2532339899
3.3292-3.40160.30091660.2522329698
3.4016-3.48070.29871850.2375337099
3.4807-3.56770.2661850.2323329699
3.5677-3.66420.24941900.2118338299
3.6642-3.77190.23021610.206331899
3.7719-3.89360.2371760.205333799
3.8936-4.03270.231870.2072337199
4.0327-4.19410.21811670.189334699
4.1941-4.38490.2111630.1808333599
4.3849-4.61590.22511490.1856337899
4.6159-4.90490.2081720.185336399
4.9049-5.28320.2051780.1919332499
5.2832-5.81410.21271800.208338899
5.8141-6.65360.24221620.2227336499
6.6536-8.37610.21491780.1921339999
8.3761-490.18691330.1878337399

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