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- PDB-5hy1: high resolution structure of barbiturase -

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Basic information

Entry
Database: PDB / ID: 5hy1
Titlehigh resolution structure of barbiturase
ComponentsBarbiturase
KeywordsHYDROLASE / Toblerone fold / pyrimidine catabolism
Function / homology
Function and homology information


barbiturase / barbiturase activity / uracil catabolic process / metal ion binding
Similarity search - Function
Cyanuric acid hydrolase/Barbituras, RU C / Cyanuric acid hydrolase/Barbiturase, RU A / Cyanuric acid hydrolase/Barbiturase / Cyanuric acid hydrolase/Barbiturase, repeating unit B / Cyanuric acid hydrolase/Barbiturase, repeating unit C / Cyanuric acid hydrolase/Barbiturase, repeating unit A / Amidohydrolase ring-opening protein (Amido_AtzD_TrzD) / 60s Ribosomal Protein L30; Chain: A; / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
1,3,5-triazine-2,4,6-triol / Barbiturase
Similarity search - Component
Biological speciesRhodococcus erythropolis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsPeat, T.S. / Scott, C. / Balotra, S. / Wilding, M. / Newman, J.
CitationJournal: Appl. Environ. Microbiol. / Year: 2017
Title: High-Resolution X-Ray Structures of Two Functionally Distinct Members of the Cyclic Amide Hydrolase Family of Toblerone Fold Enzymes.
Authors: Peat, T.S. / Balotra, S. / Wilding, M. / Hartley, C.J. / Newman, J. / Scott, C.
History
DepositionFeb 1, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 1, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 15, 2017Group: Database references
Revision 1.2Apr 26, 2017Group: Database references
Revision 1.3Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Barbiturase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4476
Polymers41,1881
Non-polymers2585
Water4,071226
1
A: Barbiturase
hetero molecules

A: Barbiturase
hetero molecules

A: Barbiturase
hetero molecules

A: Barbiturase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,78624
Polymers164,7534
Non-polymers1,03420
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_775-x+2,-y+2,z1
crystal symmetry operation3_755-x+2,y,-z1
crystal symmetry operation4_575x,-y+2,-z1
Buried area13020 Å2
ΔGint-138 kcal/mol
Surface area48920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.403, 82.356, 114.552
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-509-

HOH

21A-661-

HOH

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Components

#1: Protein Barbiturase


Mass: 41188.172 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus erythropolis (bacteria) / Gene: bar / Plasmid: pET14b variant / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q8RSQ2, barbiturase
#2: Chemical ChemComp-WDL / 1,3,5-triazine-2,4,6-triol / Cyanuric Acid


Mass: 129.074 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H3N3O3
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 226 / 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: 1.99 Å3/Da / Density % sol: 38.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Protein at 16 mg/,mL in 50 mM ADA pH 6.5, 50 mM NaCl mixed with 2.45 M ammonium sulfate, 10% glycerol; 150 nL plus 150 nL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 30, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.01→41.2 Å / Num. obs: 22146 / % possible obs: 99.6 % / Redundancy: 14.4 % / Net I/σ(I): 24.6
Reflection shellResolution: 2.01→2.06 Å / Redundancy: 13.5 % / Mean I/σ(I) obs: 3.5 / % possible all: 95.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HWE

5hwe


Resolution: 2.01→41.2 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.925 / SU B: 4.557 / SU ML: 0.125 / Cross valid method: THROUGHOUT / ESU R: 0.218 / ESU R Free: 0.172 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22273 1061 4.8 %RANDOM
Rwork0.1858 ---
obs0.1876 21081 99.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 28.651 Å2
Baniso -1Baniso -2Baniso -3
1-0.95 Å20 Å20 Å2
2---0.77 Å20 Å2
3----0.19 Å2
Refinement stepCycle: 1 / Resolution: 2.01→41.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2703 0 13 226 2942
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0192814
X-RAY DIFFRACTIONr_bond_other_d0.0030.022681
X-RAY DIFFRACTIONr_angle_refined_deg1.1961.9583835
X-RAY DIFFRACTIONr_angle_other_deg0.9636175
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0245377
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.64524.348115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.89615455
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6571520
X-RAY DIFFRACTIONr_chiral_restr0.0630.2447
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213270
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02584
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.7123.5831496
X-RAY DIFFRACTIONr_mcbond_other2.7133.581495
X-RAY DIFFRACTIONr_mcangle_it3.6396.0211877
X-RAY DIFFRACTIONr_mcangle_other3.6386.0241878
X-RAY DIFFRACTIONr_scbond_it3.3094.0631317
X-RAY DIFFRACTIONr_scbond_other3.3084.0631318
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.7496.641950
X-RAY DIFFRACTIONr_long_range_B_refined6.30714.89112565
X-RAY DIFFRACTIONr_long_range_B_other6.27414.8712397
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.011→2.063 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 69 -
Rwork0.234 1494 -
obs--95.77 %

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