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- PDB-5hxu: Structure-function analysis of functionally diverse members of th... -

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Basic information

Entry
Database: PDB / ID: 5hxu
TitleStructure-function analysis of functionally diverse members of the cyclic amide hydrolase family of Toblerone fold enzymes
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: 1.83 Å
AuthorsPeat, T.S. / Balotra, S. / Wilding, M. / Newman, J. / 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 31, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Barbiturase
B: Barbiturase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,16211
Polymers82,3762
Non-polymers7859
Water11,115617
1
A: Barbiturase
B: Barbiturase
hetero molecules

A: Barbiturase
B: Barbiturase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,32322
Polymers164,7534
Non-polymers1,57118
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area14970 Å2
ΔGint-148 kcal/mol
Surface area48000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.415, 83.415, 216.234
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-802-

HOH

21B-735-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 3 - 367 / Label seq-ID: 23 - 387

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Barbiturase


Mass: 41188.172 Da / Num. of mol.: 2
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

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Non-polymers , 5 types, 626 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-MHA / (CARBAMOYLMETHYL-CARBOXYMETHYL-AMINO)-ACETIC ACID / N-(2-ACETAMIDO)IMINODIACETIC ACID


Mass: 190.154 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H10N2O5 / Comment: pH buffer*YM
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 617 / 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: 2.43 Å3/Da / Density % sol: 49.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9
Details: Protein at 15 mg/mL; reservoir was 2.5 M ammonium sulfate with 10% (v/v) MMT buffer at pH 9; sitting drop setup with 150 nL plus 150 nL drops; crystals cryo-protected with AP/E core 150 ...Details: Protein at 15 mg/mL; reservoir was 2.5 M ammonium sulfate with 10% (v/v) MMT buffer at pH 9; sitting drop setup with 150 nL plus 150 nL drops; crystals cryo-protected with AP/E core 150 basestock (Mobile 1, Australia).

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 1.28221 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 18, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28221 Å / Relative weight: 1
ReflectionResolution: 1.83→45.7 Å / Num. obs: 67015 / % possible obs: 98.1 % / Redundancy: 26.6 % / Net I/σ(I): 22.2
Reflection shellResolution: 1.83→1.87 Å / Redundancy: 20.5 % / Mean I/σ(I) obs: 3.5 / % possible all: 81

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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: 1.83→41.5 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.89 / SU B: 3.122 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R: 0.16 / ESU R Free: 0.149 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25165 3218 4.9 %RANDOM
Rwork0.21067 ---
obs0.21268 62328 96.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 25.162 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å2-0 Å2-0 Å2
2--0.07 Å2-0 Å2
3----0.13 Å2
Refinement stepCycle: 1 / Resolution: 1.83→41.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5432 0 45 617 6094
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0195596
X-RAY DIFFRACTIONr_bond_other_d0.010.025356
X-RAY DIFFRACTIONr_angle_refined_deg1.7291.9637613
X-RAY DIFFRACTIONr_angle_other_deg1.594312335
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8645742
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.21124.348230
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.81815911
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1841542
X-RAY DIFFRACTIONr_chiral_restr0.1060.2894
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0216428
X-RAY DIFFRACTIONr_gen_planes_other0.0070.021162
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_it3.1093.0192959
X-RAY DIFFRACTIONr_mcbond_other3.1093.0192958
X-RAY DIFFRACTIONr_mcangle_it3.9675.0643704
X-RAY DIFFRACTIONr_mcangle_other3.9675.0643705
X-RAY DIFFRACTIONr_scbond_it4.3273.5882637
X-RAY DIFFRACTIONr_scbond_other4.3143.5882635
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.0825.7953909
X-RAY DIFFRACTIONr_long_range_B_refined7.19812.81525546
X-RAY DIFFRACTIONr_long_range_B_other7.10512.73424890
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 42962 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.13 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.83→1.877 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 206 -
Rwork0.237 3801 -
obs--81.13 %

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