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- PDB-6xje: Triuret Hydrolase (TrtA) from Herbaspirillum sp. BH-1 C162S bound... -

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Basic information

Entry
Database: PDB / ID: 6xje
TitleTriuret Hydrolase (TrtA) from Herbaspirillum sp. BH-1 C162S bound with triuret
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 domain
Similarity search - Domain/homology
tricarbonodiimidic diamide / Triuret hydrolase TrtA
Similarity search - Component
Biological speciesHerbaspirillum sp. BH-1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 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 23, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,49510
Polymers96,7874
Non-polymers7096
Water7,314406
1
A: Cysteine hydrolase
B: Cysteine hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7485
Polymers48,3932
Non-polymers3543
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3570 Å2
ΔGint-9 kcal/mol
Surface area16370 Å2
MethodPISA
2
C: Cysteine hydrolase
D: Cysteine hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7485
Polymers48,3932
Non-polymers3543
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3550 Å2
ΔGint-8 kcal/mol
Surface area16460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.530, 114.440, 142.930
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Cysteine hydrolase / triuret hydrolase


Mass: 24196.664 Da / Num. of mol.: 4 / Mutation: C162S
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-TIU / tricarbonodiimidic diamide


Mass: 146.105 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H6N4O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 406 / 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: 2.18 Å3/Da / Density % sol: 43.5 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1 uL 20 mg/mL protein + 1 uL 24% w/v PEG6000, 0.1 M Bis-Tris propane, 1 mM triuret, pH 8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03332 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 27, 2018
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03332 Å / Relative weight: 1
ReflectionResolution: 1.45→60.62 Å / Num. obs: 150183 / % possible obs: 100 % / Redundancy: 7.47 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 20.99
Reflection shellResolution: 1.45→1.55 Å / Redundancy: 7.21 % / Rmerge(I) obs: 0.547 / Mean I/σ(I) obs: 3.97 / Num. unique obs: 26952 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSBUILT=20180409data reduction
XDSBUILT=20180409data scaling
MOLREP11phasing
Coot0.8.9.2model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6XIX

6xix


Resolution: 1.45→60.616 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.093 / SU ML: 0.042 / Cross valid method: THROUGHOUT / ESU R: 0.064 / ESU R Free: 0.063
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1898 7510 5.001 %
Rwork0.172 142673 -
all0.173 --
obs-150183 99.957 %
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: 19.158 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å2-0 Å2-0 Å2
2---0.549 Å20 Å2
3---0.629 Å2
Refinement stepCycle: LAST / Resolution: 1.45→60.616 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6698 0 48 406 7152
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0136994
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176606
X-RAY DIFFRACTIONr_angle_refined_deg1.8731.6499521
X-RAY DIFFRACTIONr_angle_other_deg1.5941.57515274
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3675902
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.70621.003369
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.733151140
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3241565
X-RAY DIFFRACTIONr_chiral_restr0.1010.2913
X-RAY DIFFRACTIONr_gen_planes_refined0.020.027984
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021463
X-RAY DIFFRACTIONr_nbd_refined0.2190.21244
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1860.26183
X-RAY DIFFRACTIONr_nbtor_refined0.1640.23482
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0860.23158
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.2315
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1640.210
X-RAY DIFFRACTIONr_nbd_other0.2250.260
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1420.27
X-RAY DIFFRACTIONr_mcbond_it1.7031.8233578
X-RAY DIFFRACTIONr_mcbond_other1.6961.8223577
X-RAY DIFFRACTIONr_mcangle_it2.3562.7294490
X-RAY DIFFRACTIONr_mcangle_other2.3592.734491
X-RAY DIFFRACTIONr_scbond_it3.0832.1593416
X-RAY DIFFRACTIONr_scbond_other3.0832.1593417
X-RAY DIFFRACTIONr_scangle_it4.5463.125031
X-RAY DIFFRACTIONr_scangle_other4.5463.125032
X-RAY DIFFRACTIONr_lrange_it5.31822.2547539
X-RAY DIFFRACTIONr_lrange_other5.31822.2587540
X-RAY DIFFRACTIONr_ncsr_local_group_10.0810.056956
X-RAY DIFFRACTIONr_ncsr_local_group_20.0790.056935
X-RAY DIFFRACTIONr_ncsr_local_group_30.10.056849
X-RAY DIFFRACTIONr_ncsr_local_group_40.0870.056838
X-RAY DIFFRACTIONr_ncsr_local_group_50.0840.056856
X-RAY DIFFRACTIONr_ncsr_local_group_60.0930.056811
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
1.45-1.4880.3155490.288104250.289109760.8770.88299.98180.257
1.488-1.5280.2975360.257101760.259107140.8860.90199.98130.228
1.528-1.5730.2425220.22699160.227104400.9190.92299.98080.198
1.573-1.6210.2265060.19796240.198101300.9290.9341000.173
1.621-1.6740.2124920.18293500.18498430.940.94699.98980.16
1.674-1.7330.2124740.17990070.18194810.9430.9521000.16
1.733-1.7980.2094600.17687400.17892010.9420.95499.98910.16
1.798-1.8720.1954430.17384110.17488550.9490.95799.98870.161
1.872-1.9550.1934250.17780720.17884990.9540.95999.97650.17
1.955-2.050.214080.17777630.17981730.9470.95799.97550.173
2.05-2.1610.2073880.17473700.17677580.9510.9571000.176
2.161-2.2920.1923670.16569600.16673280.9570.96499.98640.171
2.292-2.450.1723460.1665850.16169340.9650.96799.95670.171
2.45-2.6460.1643220.15961090.15964350.9680.96899.93780.174
2.646-2.8980.1842980.16556730.16659740.9590.96299.94980.184
2.898-3.2390.1752720.1751680.1754450.9610.96299.90820.194
3.239-3.7380.1722400.16145530.16148000.9660.96899.85420.188
3.738-4.5740.1482050.14439010.14541120.9760.97599.85410.178
4.574-6.450.1861620.16930770.1732420.970.97699.90750.215
6.45-60.6160.206950.18117940.18319070.9680.96899.05610.246

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