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

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Basic information

Entry
Database: PDB / ID: 5hwe
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/Barbiturase, RU B / 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
(CARBAMOYLMETHYL-CARBOXYMETHYL-AMINO)-ACETIC ACID / Barbiturase
Similarity search - Component
Biological speciesRhodococcus erythropolis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 Å
AuthorsPeat, T.S. / Scott, C.
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
DepositionJan 29, 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)41,4994
Polymers41,1881
Non-polymers3113
Water5,314295
1
A: Barbiturase
hetero molecules

A: Barbiturase
hetero molecules

A: Barbiturase
hetero molecules

A: Barbiturase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,99516
Polymers164,7534
Non-polymers1,24212
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
Buried area14420 Å2
ΔGint-71 kcal/mol
Surface area50250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.341, 82.563, 114.300
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-742-

HOH

21A-744-

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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-MHA / (CARBAMOYLMETHYL-CARBOXYMETHYL-AMINO)-ACETIC ACID / N-(2-ACETAMIDO)IMINODIACETIC ACID


Mass: 190.154 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H10N2O5 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 295 / 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: 2.13 Å3/Da / Density % sol: 42.15 %
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; reservoir of 2.45 M ammonium sulfate, 10% glycerol

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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 21, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.707→41.5 Å / Num. obs: 36498 / % possible obs: 99.7 % / Redundancy: 7.2 % / Net I/σ(I): 13.2
Reflection shellResolution: 1.707→1.74 Å / Redundancy: 6.4 % / Mean I/σ(I) obs: 2.3 / % possible all: 93.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BVQ

4bvq


Resolution: 1.71→41.5 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.949 / SU B: 2.17 / SU ML: 0.07 / Cross valid method: THROUGHOUT / ESU R: 0.098 / ESU R Free: 0.101 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19447 1762 4.8 %RANDOM
Rwork0.15078 ---
obs0.15289 34725 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 19.557 Å2
Baniso -1Baniso -2Baniso -3
1--0.27 Å2-0 Å20 Å2
2---0.05 Å2-0 Å2
3---0.32 Å2
Refinement stepCycle: LAST / Resolution: 1.71→41.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2742 0 19 295 3056
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0192883
X-RAY DIFFRACTIONr_bond_other_d0.0030.022759
X-RAY DIFFRACTIONr_angle_refined_deg1.9121.9613933
X-RAY DIFFRACTIONr_angle_other_deg1.10636361
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6475388
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.55224.407118
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.22415470
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4821521
X-RAY DIFFRACTIONr_chiral_restr0.1250.2460
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213351
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02604
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_it2.3592.2461528
X-RAY DIFFRACTIONr_mcbond_other2.3552.2431527
X-RAY DIFFRACTIONr_mcangle_it3.1543.7691924
X-RAY DIFFRACTIONr_mcangle_other3.1553.7731925
X-RAY DIFFRACTIONr_scbond_it3.6862.8261353
X-RAY DIFFRACTIONr_scbond_other3.6882.8271351
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.2754.5232007
X-RAY DIFFRACTIONr_long_range_B_refined6.059.67912941
X-RAY DIFFRACTIONr_long_range_B_other6.0519.67812937
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.707→1.751 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.236 112 -
Rwork0.225 2522 -
obs--98.8 %

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