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Entry
Database: PDB / ID: 5bk6
TitleStructural and biochemical characterization of a non-canonical biuret hydrolase (BiuH) from the cyanuric acid catabolism pathway of Rhizobium leguminasorum bv. viciae 3841
ComponentsPutative amidase
KeywordsHYDROLASE / s-triazine / xenobiotic
Function / homologybiuret amidohydrolase / : / Isochorismatase-like / Isochorismatase-like superfamily / Isochorismatase domain / hydrolase activity / Biuret amidohydrolase
Function and homology information
Biological speciesRhizobium leguminosarum bv. viciae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 Å
AuthorsPeat, T.S. / Esquirol, L. / Newman, J. / Scott, C.
CitationJournal: PLoS ONE / Year: 2018
Title: Structural and biochemical characterization of the biuret hydrolase (BiuH) from the cyanuric acid catabolism pathway of Rhizobium leguminasorum bv. viciae 3841.
Authors: Esquirol, L. / Peat, T.S. / Wilding, M. / Lucent, D. / French, N.G. / Hartley, C.J. / Newman, J. / Scott, C.
History
DepositionSep 12, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 21, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 27, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Putative amidase
B: Putative amidase
C: Putative amidase
D: Putative amidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,75211
Polymers114,6394
Non-polymers1,1137
Water17,276959
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14570 Å2
ΔGint4 kcal/mol
Surface area28690 Å2
2
A: Putative amidase
D: Putative amidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,9226
Polymers57,3192
Non-polymers6034
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4640 Å2
ΔGint-5 kcal/mol
Surface area17270 Å2
MethodPISA
3
B: Putative amidase
C: Putative amidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,8305
Polymers57,3192
Non-polymers5113
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4580 Å2
ΔGint-5 kcal/mol
Surface area16780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.130, 122.678, 135.745
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11D-619-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASNASNLEULEUAA8 - 23228 - 252
21ASNASNLEULEUBB8 - 23228 - 252
12METMETPROPROAA4 - 23324 - 253
22METMETPROPROCC4 - 23324 - 253
13ASNASNLEULEUAA8 - 23228 - 252
23ASNASNLEULEUDD8 - 23228 - 252
14ASNASNLEULEUBB8 - 23228 - 252
24ASNASNLEULEUCC8 - 23228 - 252
15ASNASNPROPROBB8 - 23328 - 253
25ASNASNPROPRODD8 - 23328 - 253
16ASNASNLEULEUCC8 - 23228 - 252
26ASNASNLEULEUDD8 - 23228 - 252

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Putative amidase


Mass: 28659.643 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhizobium leguminosarum bv. viciae (strain 3841) (bacteria)
Strain: 3841 / Gene: pRL100352 / Plasmid: pETcc2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / Variant (production host): DE3 / References: UniProt: Q1M7F4
#2: Chemical
ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C8H19NO5 / Comment: pH buffer*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 959 / 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: 2.58 Å3/Da / Density % sol: 52.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: Sitting drops were set up with 150 nL protein at 100 mg/mL plus 150 nL reservoir: 100 mM bis-tris chloride buffer at pH 5.5, 17% (w/v) PEG 10000, 100 mM sodium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95373 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 29, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 1.59→45.8 Å / Num. obs: 139814 / % possible obs: 100 % / Redundancy: 6.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.045 / Net I/σ(I): 11.7
Reflection shellResolution: 1.59→1.62 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.726 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 6816 / CC1/2: 0.627 / Rpim(I) all: 0.588 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6AZN

6azn


Resolution: 1.59→45.8 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.46 / SU ML: 0.049 / Cross valid method: THROUGHOUT / ESU R: 0.07 / ESU R Free: 0.07 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1742 6886 4.9 %RANDOM
Rwork0.15004 ---
obs0.15124 132830 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 22.091 Å2
Baniso -1Baniso -2Baniso -3
1--0.28 Å2-0 Å20 Å2
2--0.43 Å2-0 Å2
3----0.16 Å2
Refinement stepCycle: 1 / Resolution: 1.59→45.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6992 0 74 959 8025
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0197505
X-RAY DIFFRACTIONr_bond_other_d0.0020.026915
X-RAY DIFFRACTIONr_angle_refined_deg1.8931.97210216
X-RAY DIFFRACTIONr_angle_other_deg1.144316077
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2315968
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.74923.686331
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.883151212
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.311559
X-RAY DIFFRACTIONr_chiral_restr0.130.21108
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0218501
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021494
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_it1.8092.0133803
X-RAY DIFFRACTIONr_mcbond_other1.8072.0123802
X-RAY DIFFRACTIONr_mcangle_it2.4653.0094794
X-RAY DIFFRACTIONr_mcangle_other2.4653.0094795
X-RAY DIFFRACTIONr_scbond_it2.9682.2993702
X-RAY DIFFRACTIONr_scbond_other2.9682.2993702
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.3053.3425423
X-RAY DIFFRACTIONr_long_range_B_refined5.31239.85733870
X-RAY DIFFRACTIONr_long_range_B_other5.31139.85633868
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A152040.07
12B152040.07
21A155160.07
22C155160.07
31A152300.07
32D152300.07
41B152320.07
42C152320.07
51B155040.05
52D155040.05
61C152400.08
62D152400.08
LS refinement shellResolution: 1.59→1.631 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.26 493 -
Rwork0.253 9718 -
obs--99.93 %

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