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- PDB-6xk1: Biuret Hydrolase (BiuH) from Rhodococcus sp. Mel C169S Apo form -

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Basic information

Entry
Database: PDB / ID: 6xk1
TitleBiuret Hydrolase (BiuH) from Rhodococcus sp. Mel C169S Apo form
ComponentsBiuret hydrolase
KeywordsHYDROLASE / TrtA / BiuH / triuret / biuret / cysteine hydrolase / nitrogen
Function / homology: / Isochorismatase-like / Isochorismatase-like superfamily / Isochorismatase domain / hydrolase activity / Biuret hydrolase
Function and homology information
Biological speciesRhodococcus sp. Mel (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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 25, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 18, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 14, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _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: Biuret hydrolase
B: Biuret hydrolase
C: Biuret hydrolase
D: Biuret hydrolase


Theoretical massNumber of molelcules
Total (without water)104,1774
Polymers104,1774
Non-polymers00
Water9,170509
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, dimer of dimers
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12000 Å2
ΔGint-30 kcal/mol
Surface area27710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.100, 104.400, 135.300
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11Chains AAA BBB
21Chains AAA CCC
31Chains AAA DDD
41Chains BBB CCC
51Chains BBB DDD
61Chains CCC DDD

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Components

#1: Protein
Biuret hydrolase / cysteine hydrolase


Mass: 26044.336 Da / Num. of mol.: 4 / Mutation: C169S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus sp. Mel (bacteria) / Gene: biuH / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: H8ZKV9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 509 / 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: 2.1 Å3/Da / Density % sol: 41.39 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 1uL 10mg/mL protein + 1uL 18% w/v PEG3350, 0.2M MgCl2, 1mM triuret pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.99184 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 15, 2020
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99184 Å / Relative weight: 1
ReflectionResolution: 1.7→82.66 Å / Num. obs: 186186 / % possible obs: 99.6 % / Redundancy: 3.85 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 11.55
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 3.77 % / Rmerge(I) obs: 0.501 / Mean I/σ(I) obs: 2.96 / Num. unique obs: 29499 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSBUILT=20200131data reduction
XSCALEBUILT=20200131data scaling
MOLREP11phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6XJM

6xjm


Resolution: 1.7→56.837 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.951 / WRfactor Rfree: 0.21 / WRfactor Rwork: 0.185 / SU B: 2.108 / SU ML: 0.069 / Average fsc free: 0.9342 / Average fsc work: 0.9422 / Cross valid method: THROUGHOUT / ESU R: 0.109 / ESU R Free: 0.102
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2079 4864 5 %
Rwork0.1844 92409 -
all0.186 --
obs-97273 99.858 %
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: 18.828 Å2
Baniso -1Baniso -2Baniso -3
1-0.838 Å2-0 Å20 Å2
2---0.422 Å2-0 Å2
3----0.416 Å2
Refinement stepCycle: LAST / Resolution: 1.7→56.837 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6856 0 0 509 7365
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0137013
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176459
X-RAY DIFFRACTIONr_angle_refined_deg1.6471.6459562
X-RAY DIFFRACTIONr_angle_other_deg1.3941.57514926
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9895907
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.12120.575348
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.261151073
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8821560
X-RAY DIFFRACTIONr_chiral_restr0.0850.2950
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.027985
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021483
X-RAY DIFFRACTIONr_nbd_refined0.2070.21170
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1880.25675
X-RAY DIFFRACTIONr_nbtor_refined0.1490.23397
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.22684
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1130.2296
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1120.24
X-RAY DIFFRACTIONr_nbd_other0.1780.224
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3060.23
X-RAY DIFFRACTIONr_mcbond_it1.5351.8933640
X-RAY DIFFRACTIONr_mcbond_other1.5341.8923639
X-RAY DIFFRACTIONr_mcangle_it2.1062.8324543
X-RAY DIFFRACTIONr_mcangle_other2.1062.8334544
X-RAY DIFFRACTIONr_scbond_it2.2342.083373
X-RAY DIFFRACTIONr_scbond_other2.2342.0813374
X-RAY DIFFRACTIONr_scangle_it3.2063.0415019
X-RAY DIFFRACTIONr_scangle_other3.2063.0425020
X-RAY DIFFRACTIONr_lrange_it4.06422.47494
X-RAY DIFFRACTIONr_lrange_other4.04322.2417411
X-RAY DIFFRACTIONr_ncsr_local_group_10.0650.056958
X-RAY DIFFRACTIONr_ncsr_local_group_20.0620.056978
X-RAY DIFFRACTIONr_ncsr_local_group_30.0670.056989
X-RAY DIFFRACTIONr_ncsr_local_group_40.0660.056973
X-RAY DIFFRACTIONr_ncsr_local_group_50.0720.056966
X-RAY DIFFRACTIONr_ncsr_local_group_60.0710.057029
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.7440.2953570.2796788X-RAY DIFFRACTION99.958
1.744-1.7920.2553460.236575X-RAY DIFFRACTION100
1.792-1.8440.243390.2156436X-RAY DIFFRACTION100
1.844-1.9010.2383280.2036226X-RAY DIFFRACTION99.9542
1.901-1.9630.263170.2296036X-RAY DIFFRACTION99.9371
1.963-2.0320.2363080.1895844X-RAY DIFFRACTION99.9188
2.032-2.1080.2252970.1965646X-RAY DIFFRACTION99.8824
2.108-2.1940.2362870.1975444X-RAY DIFFRACTION99.8084
2.194-2.2920.2412750.1995236X-RAY DIFFRACTION99.7466
2.292-2.4040.2042620.1754978X-RAY DIFFRACTION99.7146
2.404-2.5340.2132510.1724766X-RAY DIFFRACTION99.7217
2.534-2.6870.2242380.1824517X-RAY DIFFRACTION99.7483
2.687-2.8720.2012240.1764259X-RAY DIFFRACTION99.8219
2.872-3.1020.22100.1873983X-RAY DIFFRACTION99.8096
3.102-3.3980.1961920.1853654X-RAY DIFFRACTION99.8183
3.398-3.7980.1841760.1723342X-RAY DIFFRACTION99.8581
3.798-4.3840.1421560.1432973X-RAY DIFFRACTION99.6814
4.384-5.3660.1461330.1472529X-RAY DIFFRACTION99.85
5.366-7.5720.2151060.1812003X-RAY DIFFRACTION100

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