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- PDB-6azq: Structural and biochemical characterization of a non-canonical bi... -

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Basic information

Entry
Database: PDB / ID: 6azq
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 / dicarbonimidic diamide / Biuret amidohydrolase
Function and homology information
Biological speciesRhizobium leguminosarum bv. viciae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.22 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 11, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 21, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 4, 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
G: Putative amidase
H: Putative amidase
A: Putative amidase
B: Putative amidase
C: Putative amidase
D: Putative amidase
E: Putative amidase
F: Putative amidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)229,99920
Polymers229,0778
Non-polymers92212
Water7,368409
1
G: Putative amidase
H: Putative amidase
C: Putative amidase
D: Putative amidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,07111
Polymers114,5384
Non-polymers5337
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12420 Å2
ΔGint-60 kcal/mol
Surface area27080 Å2
MethodPISA
2
A: Putative amidase
B: Putative amidase
E: Putative amidase
F: Putative amidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,9289
Polymers114,5384
Non-polymers3895
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12150 Å2
ΔGint-54 kcal/mol
Surface area27370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.702, 87.303, 341.695
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11G
21H
12G
22A
13G
23B
14G
24C
15G
25D
16G
26E
17G
27F
18H
28A
19H
29B
110H
210C
111H
211D
112H
212E
113H
213F
114A
214B
115A
215C
116A
216D
117A
217E
118A
218F
119B
219C
120B
220D
121B
221E
122B
222F
123C
223D
124C
224E
125C
225F
126D
226E
127D
227F
128E
228F

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
11ASNASNPROPROGA8 - 23328 - 253
21ASNASNPROPROHB8 - 23328 - 253
12ASNASNPROPROGA8 - 23328 - 253
22ASNASNPROPROAC8 - 23328 - 253
13ASNASNPROPROGA8 - 23328 - 253
23ASNASNPROPROBD8 - 23328 - 253
14ARGARGLEULEUGA9 - 23229 - 252
24ARGARGLEULEUCE9 - 23229 - 252
15ASNASNPROPROGA8 - 23328 - 253
25ASNASNPROPRODF8 - 23328 - 253
16ASNASNPROPROGA8 - 23328 - 253
26ASNASNPROPROEG8 - 23328 - 253
17ARGARGLEULEUGA9 - 23229 - 252
27ARGARGLEULEUFH9 - 23229 - 252
18ASNASNPROPROHB8 - 23328 - 253
28ASNASNPROPROAC8 - 23328 - 253
19ASNASNPROPROHB8 - 23328 - 253
29ASNASNPROPROBD8 - 23328 - 253
110ARGARGLEULEUHB9 - 23229 - 252
210ARGARGLEULEUCE9 - 23229 - 252
111ASNASNPROPROHB8 - 23328 - 253
211ASNASNPROPRODF8 - 23328 - 253
112ASNASNPROPROHB8 - 23328 - 253
212ASNASNPROPROEG8 - 23328 - 253
113ARGARGLEULEUHB9 - 23229 - 252
213ARGARGLEULEUFH9 - 23229 - 252
114ASNASNPROPROAC8 - 23328 - 253
214ASNASNPROPROBD8 - 23328 - 253
115ARGARGLEULEUAC9 - 23229 - 252
215ARGARGLEULEUCE9 - 23229 - 252
116ASNASNPROPROAC8 - 23328 - 253
216ASNASNPROPRODF8 - 23328 - 253
117ASNASNPROPROAC8 - 23328 - 253
217ASNASNPROPROEG8 - 23328 - 253
118ARGARGLEULEUAC9 - 23229 - 252
218ARGARGLEULEUFH9 - 23229 - 252
119ARGARGLEULEUBD9 - 23229 - 252
219ARGARGLEULEUCE9 - 23229 - 252
120ASNASNPROPROBD8 - 23328 - 253
220ASNASNPROPRODF8 - 23328 - 253
121ASNASNPROPROBD8 - 23328 - 253
221ASNASNPROPROEG8 - 23328 - 253
122ARGARGLEULEUBD9 - 23229 - 252
222ARGARGLEULEUFH9 - 23229 - 252
123ARGARGLEULEUCE9 - 23229 - 252
223ARGARGLEULEUDF9 - 23229 - 252
124ARGARGLEULEUCE9 - 23229 - 252
224ARGARGLEULEUEG9 - 23229 - 252
125ARGARGPROPROCE9 - 23329 - 253
225ARGARGPROPROFH9 - 23329 - 253
126ASNASNPROPRODF8 - 23328 - 253
226ASNASNPROPROEG8 - 23328 - 253
127ARGARGLEULEUDF9 - 23229 - 252
227ARGARGLEULEUFH9 - 23229 - 252
128ARGARGLEULEUEG9 - 23229 - 252
228ARGARGLEULEUFH9 - 23229 - 252

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28

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Components

#1: Protein
Putative amidase


Mass: 28634.611 Da / Num. of mol.: 8
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-C5J / dicarbonimidic diamide


Mass: 103.080 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H5N3O2
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 409 / 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: 2.4 Å3/Da / Density % sol: 48.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: Sitting drops were set up with 200 nL protein at 13 mg/mL plus 200 nL reservoir: 11.9% (w/v) PEG 8000, 27 mM calcium chloride, 100 mM citrate buffer at pH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 8, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.22→47.7 Å / Num. obs: 110156 / % possible obs: 99.9 % / Redundancy: 7.4 % / CC1/2: 0.99 / Rmerge(I) obs: 0.159 / Rpim(I) all: 0.093 / Net I/σ(I): 7.7
Reflection shellResolution: 2.22→2.26 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.726 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 5317 / CC1/2: 0.652 / Rpim(I) all: 0.434 / % possible all: 98.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6azn

6azn


Resolution: 2.22→42.85 Å / Cor.coef. Fo:Fc: 0.894 / Cor.coef. Fo:Fc free: 0.873 / SU B: 8.695 / SU ML: 0.212 / Cross valid method: THROUGHOUT / ESU R: 0.311 / ESU R Free: 0.232 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27744 5462 5 %RANDOM
Rwork0.24901 ---
obs0.25044 104573 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 32.755 Å2
Baniso -1Baniso -2Baniso -3
1-1.45 Å2-0 Å20 Å2
2---1.07 Å2-0 Å2
3----0.37 Å2
Refinement stepCycle: 1 / Resolution: 2.22→42.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13849 0 54 409 14312
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01914270
X-RAY DIFFRACTIONr_bond_other_d0.0020.0213278
X-RAY DIFFRACTIONr_angle_refined_deg1.4331.9719363
X-RAY DIFFRACTIONr_angle_other_deg1.019330795
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.00551816
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.71223.645620
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.12152346
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.12515112
X-RAY DIFFRACTIONr_chiral_restr0.0940.22119
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02116012
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022804
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_it2.3143.277261
X-RAY DIFFRACTIONr_mcbond_other2.3133.277260
X-RAY DIFFRACTIONr_mcangle_it3.3884.8979078
X-RAY DIFFRACTIONr_mcangle_other3.3884.8979079
X-RAY DIFFRACTIONr_scbond_it2.2943.4087009
X-RAY DIFFRACTIONr_scbond_other2.2933.4087010
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.4215.05910286
X-RAY DIFFRACTIONr_long_range_B_refined6.07762.3761966
X-RAY DIFFRACTIONr_long_range_B_other6.07762.3761967
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)
11G152740.05
12H152740.05
21G153420.04
22A153420.04
31G152580.05
32B152580.05
41G150860.05
42C150860.05
51G152960.05
52D152960.05
61G153020.04
62E153020.04
71G151400.05
72F151400.05
81H153080.05
82A153080.05
91H153260.04
92B153260.04
101H151380.06
102C151380.06
111H153740.04
112D153740.04
121H152760.05
122E152760.05
131H152280.04
132F152280.04
141A151360.05
142B151360.05
151A149820.05
152C149820.05
161A151800.05
162D151800.05
171A151920.05
172E151920.05
181A150180.05
182F150180.05
191B150440.06
192C150440.06
201B152740.05
202D152740.05
211B152200.05
212E152200.05
221B151300.05
222F151300.05
231C151220.06
232D151220.06
241C151300.05
242E151300.05
251C151860.06
252F151860.06
261D151560.05
262E151560.05
271D150760.05
272F150760.05
281E151020.05
282F151020.05
LS refinement shellResolution: 2.22→2.278 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.357 386 -
Rwork0.322 7592 -
obs--99.63 %

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