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- PDB-6xj4: Triuret Hydrolase (TrtA) from Herbaspirillum sp. BH-1 C162S bound... -

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Basic information

Entry
Database: PDB / ID: 6xj4
TitleTriuret Hydrolase (TrtA) from Herbaspirillum sp. BH-1 C162S bound with biuret
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
dicarbonimidic diamide / Triuret hydrolase TrtA
Similarity search - Component
Biological speciesHerbaspirillum sp. BH-1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,20010
Polymers96,7874
Non-polymers4136
Water7,422412
1
A: Cysteine hydrolase
B: Cysteine hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6836
Polymers48,3932
Non-polymers2894
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3940 Å2
ΔGint-0 kcal/mol
Surface area16650 Å2
MethodPISA
2
C: Cysteine hydrolase
D: Cysteine hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5174
Polymers48,3932
Non-polymers1242
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3620 Å2
ΔGint-4 kcal/mol
Surface area17180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.630, 114.180, 141.470
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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-C5J / dicarbonimidic diamide


Mass: 103.080 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H5N3O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 412 / 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: 2.15 Å3/Da / Density % sol: 42.86 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 1uL 10 mg/mL TrtA + 1 uL 26% w/v PEG6000, 0.1 M Bis-Tris propane, 30 mM biuret, pH 9

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.992 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 12, 2019
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.992 Å / Relative weight: 1
ReflectionResolution: 1.78→57.09 Å / Num. obs: 80968 / % possible obs: 99.8 % / Redundancy: 3.85 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 12.44
Reflection shellResolution: 1.78→1.88 Å / Redundancy: 3.77 % / Rmerge(I) obs: 0.369 / Mean I/σ(I) obs: 4.26 / Num. unique obs: 23387 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
Coot0.8.9.2model building
XDSBUILT=20190315data scaling
MOLREP11phasing
XDSBUILT=20190315data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6XIX

6xix


Resolution: 1.78→57.09 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.96 / SU B: 2.072 / SU ML: 0.065 / Cross valid method: THROUGHOUT / ESU R: 0.109 / ESU R Free: 0.104
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1872 4049 5.001 %
Rwork0.1557 76919 -
all0.157 --
obs-80968 99.928 %
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: 27.334 Å2
Baniso -1Baniso -2Baniso -3
1--1.077 Å2-0 Å2-0 Å2
2---1.102 Å20 Å2
3---2.178 Å2
Refinement stepCycle: LAST / Resolution: 1.78→57.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6698 0 27 412 7137
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0136918
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176541
X-RAY DIFFRACTIONr_angle_refined_deg1.7031.6479410
X-RAY DIFFRACTIONr_angle_other_deg1.4681.56915129
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5195889
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.40721.06368
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.863151125
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5231564
X-RAY DIFFRACTIONr_chiral_restr0.0940.2905
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0387861
X-RAY DIFFRACTIONr_gen_planes_other0.0140.091427
X-RAY DIFFRACTIONr_nbd_refined0.210.21242
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1890.26108
X-RAY DIFFRACTIONr_nbtor_refined0.1580.23449
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.23071
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.2321
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1550.211
X-RAY DIFFRACTIONr_nbd_other0.2040.253
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2350.28
X-RAY DIFFRACTIONr_mcbond_it2.2772.6393544
X-RAY DIFFRACTIONr_mcbond_other2.2592.6383543
X-RAY DIFFRACTIONr_mcangle_it2.9683.9444437
X-RAY DIFFRACTIONr_mcangle_other2.9683.9444438
X-RAY DIFFRACTIONr_scbond_it3.853.0953374
X-RAY DIFFRACTIONr_scbond_other3.853.0963375
X-RAY DIFFRACTIONr_scangle_it5.6934.4664973
X-RAY DIFFRACTIONr_scangle_other5.6934.4674974
X-RAY DIFFRACTIONr_lrange_it6.5132.5097386
X-RAY DIFFRACTIONr_lrange_other6.40732.1847308
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
1.78-1.8260.2192940.18755850.18958790.9180.9311000.17
1.826-1.8760.2122890.17254810.17457700.9340.9431000.154
1.876-1.9310.2132810.16453540.16656370.9390.95299.96450.15
1.931-1.990.1912740.1651990.16254730.9490.9531000.147
1.99-2.0550.2022640.14950090.15252770.9490.96399.92420.137
2.055-2.1270.1932540.14548340.14750910.9510.9699.94110.138
2.127-2.2070.1882470.14346970.14649460.9550.96699.95960.139
2.207-2.2970.1762390.14645270.14847700.9610.96599.91610.144
2.297-2.3990.1882290.14243550.14445930.9570.96899.8040.144
2.399-2.5160.1942190.15541560.15743760.9530.96399.97710.161
2.516-2.6520.22090.14939800.15141900.9570.96899.97610.158
2.652-2.8120.171970.14637500.14739490.970.97199.94940.16
2.812-3.0060.1791880.14235700.14437580.9690.9751000.159
3.006-3.2460.1791740.15733080.15934820.9640.9661000.182
3.246-3.5550.1781610.15430550.15632170.9650.96799.96890.182
3.555-3.9730.1811470.15227990.15329540.9610.9799.72920.182
3.973-4.5830.1571300.14524560.14525920.9760.97799.76850.179
4.583-5.6040.1821110.16321130.16422290.9680.97599.77570.212
5.604-7.8880.262890.20316890.20617780.930.9531000.256
7.888-57.090.181530.17410010.17410610.9690.97199.34020.226

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