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- PDB-6s7j: Native crystal structure of ergothioneine degrading enzyme Ergoth... -

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Basic information

Entry
Database: PDB / ID: 6s7j
TitleNative crystal structure of ergothioneine degrading enzyme Ergothionase from Treponema denticola
ComponentsUncharacterized protein
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 / Histidine ammonia-lyase
Function and homology information
Biological speciesTreponema denticola SP33 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 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 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
C: Uncharacterized protein
D: Uncharacterized protein
E: Uncharacterized protein
F: Uncharacterized protein
G: Uncharacterized protein
H: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)445,5738
Polymers445,5738
Non-polymers00
Water8,215456
1
A: Uncharacterized protein
B: Uncharacterized protein
C: Uncharacterized protein
D: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)222,7874
Polymers222,7874
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27740 Å2
ΔGint-153 kcal/mol
Surface area55020 Å2
MethodPISA
2
E: Uncharacterized protein
F: Uncharacterized protein
G: Uncharacterized protein
H: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)222,7874
Polymers222,7874
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27910 Å2
ΔGint-149 kcal/mol
Surface area55210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.906, 76.956, 177.567
Angle α, β, γ (deg.)78.090, 82.020, 79.780
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Uncharacterized protein


Mass: 55696.668 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Treponema denticola SP33 (bacteria) / Gene: HMPREF9733_00339 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: M2BPW8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 456 / 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: 2.26 Å3/Da / Density % sol: 45.57 %
Crystal growTemperature: 293.5 K / Method: vapor diffusion, sitting drop / pH: 7.4 / Details: PEG 4000, PEG 200, 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: 0.999 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: May 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999 Å / Relative weight: 1
ReflectionResolution: 2.2→49.26 Å / Num. obs: 190138 / % possible obs: 96.1 % / Redundancy: 5.6 % / Biso Wilson estimate: 18.18 Å2 / CC1/2: 0.978 / Rmerge(I) obs: 0.219 / Rpim(I) all: 0.1 / Rrim(I) all: 0.242 / Net I/σ(I): 5.9 / Num. measured all: 1055507 / Scaling rejects: 738
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
2.2-2.2450.874377088320.4830.4220.9732.190.7
12.05-49.266.50.133766811870.980.0570.14511.798

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.3 Å49.33 Å
Translation5.3 Å49.33 Å

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Processing

Software
NameVersionClassificationNB
PHENIXrefinement
XDSdata reduction
Aimless0.7.4data scaling
PHASER2.8.0phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→49.26 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 28.16
RfactorNum. reflection% reflection
Rfree0.2669 9554 5.03 %
Rwork0.2166 --
obs0.2191 190034 96.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 66.02 Å2 / Biso mean: 21.2351 Å2 / Biso min: 3.34 Å2
Refinement stepCycle: final / Resolution: 2.2→49.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms31195 0 0 456 31651
Biso mean---17.99 -
Num. residues----3973
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00831747
X-RAY DIFFRACTIONf_angle_d0.94142835
X-RAY DIFFRACTIONf_chiral_restr0.0514829
X-RAY DIFFRACTIONf_plane_restr0.0065547
X-RAY DIFFRACTIONf_dihedral_angle_d7.1419387
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.2-2.2250.31192560.2511565891
2.225-2.25120.35023060.2726571590
2.2512-2.27860.32883170.2657568391
2.2786-2.30750.34863270.2522569891
2.3075-2.33780.30383020.2435576392
2.3378-2.36990.32323040.2378578193
2.3699-2.40370.30963100.2354584592
2.4037-2.43960.29522970.2391580594
2.4396-2.47770.32352960.2465591693
2.4777-2.51830.30852960.2417578294
2.5183-2.56180.31272950.2348596894
2.5618-2.60840.29663070.2239576194
2.6084-2.65850.27192790.2242605994
2.6585-2.71280.28663180.2366584495
2.7128-2.77180.31663450.2364603096
2.7718-2.83620.28893370.2313610697
2.8362-2.90720.29233400.2393603897
2.9072-2.98570.28593370.2279612298
2.9857-3.07360.27963040.2285630999
3.0736-3.17280.26463540.228613899
3.1728-3.28620.28023640.22256188100
3.2862-3.41770.26883190.2216235100
3.4177-3.57320.25223110.21846275100
3.5732-3.76150.24353340.19956246100
3.7615-3.99710.23873280.19316284100
3.9971-4.30550.21093160.17966293100
4.3055-4.73850.21623100.17246252100
4.7385-5.42340.21243480.18196243100
5.4234-6.83010.23853410.20526222100
6.8301-49.260.21583560.19346221100

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