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- PDB-6xix: Triuret Hydrolase (TrtA) from Herbaspirillum sp. BH-1 -

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Basic information

Entry
Database: PDB / ID: 6xix
TitleTriuret Hydrolase (TrtA) from Herbaspirillum sp. BH-1
ComponentsCysteine hydrolase
KeywordsHYDROLASE / TrtA / triuret / biuret / cysteine hydrolase / nitrogen
Function / homology
Function and homology information


amide catabolic process / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / protein homodimerization activity / identical protein binding
Similarity search - Function
Isochorismatase-like / Isochorismatase-like superfamily / Isochorismatase family
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / Triuret hydrolase TrtA
Similarity search - Component
Biological speciesHerbaspirillum sp. BH-1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsTassoulas, L.T. / Elias, M.H. / Wackett, L.P.
Funding support United States, 2items
OrganizationGrant numberCountry
United States Department of Agriculture (USDA)2019-67019-29403 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5T32GM008347-28 United States
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Discovery of an ultraspecific triuret hydrolase (TrtA) establishes the triuret biodegradation pathway.
Authors: Tassoulas, L.J. / Elias, M.H. / Wackett, L.P.
History
DepositionJun 22, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 18, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 21, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Oct 18, 2023Group: 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
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: Cysteine hydrolase
B: Cysteine hydrolase
C: Cysteine hydrolase
D: Cysteine hydrolase
E: Cysteine hydrolase
F: Cysteine hydrolase
G: Cysteine hydrolase
H: Cysteine hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)194,32716
Polymers193,7028
Non-polymers6258
Water14,106783
1
A: Cysteine hydrolase
G: Cysteine hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5824
Polymers48,4252
Non-polymers1562
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3680 Å2
ΔGint-14 kcal/mol
Surface area16820 Å2
MethodPISA
2
B: Cysteine hydrolase
E: Cysteine hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5824
Polymers48,4252
Non-polymers1562
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3660 Å2
ΔGint-13 kcal/mol
Surface area16960 Å2
MethodPISA
3
C: Cysteine hydrolase
D: Cysteine hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5824
Polymers48,4252
Non-polymers1562
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3770 Å2
ΔGint-12 kcal/mol
Surface area16850 Å2
MethodPISA
4
F: Cysteine hydrolase
H: Cysteine hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5824
Polymers48,4252
Non-polymers1562
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3730 Å2
ΔGint-14 kcal/mol
Surface area16870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.950, 76.550, 93.590
Angle α, β, γ (deg.)118.403, 89.606, 103.065
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Cysteine hydrolase / triuret hydrolase


Mass: 24212.729 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Herbaspirillum sp. BH-1 (bacteria) / Gene: HBH1_00246 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2N6JFX7
#2: Chemical
ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6OS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 783 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.3 Å3/Da / Density % sol: 46.43 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 1 uL 20 mg/mL protein + 1 uL 24% PEG6000, 0.1 M Bis-Tris propane

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 22, 2018
RadiationMonochromator: Cryogenically-cooled single crystal Si(220) side bounce
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.1→81.57 Å / Num. obs: 91216 / % possible obs: 90.4 % / Redundancy: 2.13 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 9.16
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 2.16 % / Rmerge(I) obs: 0.176 / Mean I/σ(I) obs: 4.76 / Num. unique obs: 12132 / % possible all: 92.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSBUILT=20180319data scaling
Coot0.8.9.2model building
MOLREP11phasing
XDSBUILT=20180319data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6AZO

6azo


Resolution: 2.1→70.57 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.918 / WRfactor Rfree: 0.238 / WRfactor Rwork: 0.188 / SU B: 4.894 / SU ML: 0.131 / Average fsc free: 0.9207 / Average fsc work: 0.9365 / Cross valid method: THROUGHOUT / ESU R: 0.274 / ESU R Free: 0.204
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2283 4561 5 %
Rwork0.1785 86654 -
all0.181 --
obs-91215 90.669 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 20.286 Å2
Baniso -1Baniso -2Baniso -3
1-1.444 Å20.129 Å2-2.53 Å2
2---0.294 Å2-0.795 Å2
3---0.251 Å2
Refinement stepCycle: LAST / Resolution: 2.1→70.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13411 0 32 783 14226
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01313752
X-RAY DIFFRACTIONr_bond_other_d0.0010.01713045
X-RAY DIFFRACTIONr_angle_refined_deg1.5611.64718682
X-RAY DIFFRACTIONr_angle_other_deg1.2921.56930143
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.01451758
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.8320.952735
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.997152235
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg28.14158
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.84815130
X-RAY DIFFRACTIONr_chiral_restr0.0730.21802
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215556
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022834
X-RAY DIFFRACTIONr_nbd_refined0.1960.22681
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1870.212746
X-RAY DIFFRACTIONr_nbtor_refined0.1520.26700
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.26001
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1780.2818
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0670.26
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1430.229
X-RAY DIFFRACTIONr_nbd_other0.1960.2104
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2160.220
X-RAY DIFFRACTIONr_mcbond_it1.4782.0287044
X-RAY DIFFRACTIONr_mcbond_other1.4782.0277043
X-RAY DIFFRACTIONr_mcangle_it2.253.0318798
X-RAY DIFFRACTIONr_mcangle_other2.253.0318799
X-RAY DIFFRACTIONr_scbond_it2.0332.2816708
X-RAY DIFFRACTIONr_scbond_other2.0332.2816709
X-RAY DIFFRACTIONr_scangle_it3.1913.3259884
X-RAY DIFFRACTIONr_scangle_other3.193.3259885
X-RAY DIFFRACTIONr_lrange_it4.51924.55214912
X-RAY DIFFRACTIONr_lrange_other4.42824.40714763
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.1-2.1550.253450.1965650.19274930.8930.91592.21940.177
2.155-2.2130.2523340.18763450.1972400.8910.91892.25140.176
2.213-2.2780.2273170.1860170.18370470.9170.92989.88220.17
2.278-2.3480.2613110.17159070.17568230.9060.93791.13290.163
2.348-2.4250.2222990.17556860.17766260.930.93590.3260.168
2.425-2.510.2552950.17155940.17564350.9160.93791.51520.166
2.51-2.6040.2432820.17353670.17662140.920.93890.90760.171
2.604-2.710.2622660.18650590.1959460.9040.92689.5560.186
2.71-2.8310.2472510.19147570.19457090.9030.9287.72110.194
2.831-2.9690.2282160.16841130.17154420.930.94779.5480.174
2.969-3.1290.2352370.17545100.17852160.9220.93991.00840.184
3.129-3.3180.242310.18443740.18749160.9270.93993.67370.192
3.318-3.5470.242150.19340860.19646100.9230.93593.29720.203
3.547-3.830.2072000.17438070.17543290.950.95792.56180.188
3.83-4.1940.1871820.16134510.16239320.9550.96392.39570.18
4.194-4.6870.1661640.14931250.1535860.9660.9791.71780.174
4.687-5.4090.2011410.17526800.17731590.9530.95989.30040.207
5.409-6.6140.2711170.21322190.21626690.9310.94787.52340.247
6.614-9.3130.2091010.18719190.18820610.9440.95498.01070.22
9.313-70.570.268570.22610730.22911480.9270.93198.43210.289

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