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Basic information

Entry
Database: PDB / ID: 6azn
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 family / hydrolase activity / PHOSPHATE ION / Biuret amidohydrolase
Function and homology information
Biological speciesRhizobium leguminosarum bv. viciae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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
A: Putative amidase
B: Putative amidase
C: Putative amidase
D: Putative amidase
F: Putative amidase
G: Putative amidase
H: Putative amidase
I: Putative amidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)229,61015
Polymers229,0778
Non-polymers5337
Water26,0321445
1
A: Putative amidase
B: Putative amidase
C: Putative amidase
D: Putative amidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,7587
Polymers114,5384
Non-polymers2193
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12740 Å2
ΔGint-29 kcal/mol
Surface area27710 Å2
MethodPISA
2
F: Putative amidase
G: Putative amidase
H: Putative amidase
I: Putative amidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,8538
Polymers114,5384
Non-polymers3144
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12940 Å2
ΔGint-39 kcal/mol
Surface area27700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.180, 86.921, 342.962
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
11A
21B
12A
22C
13A
23D
14A
24F
15A
25G
16A
26H
17A
27I
18B
28C
19B
29D
110B
210F
111B
211G
112B
212H
113B
213I
114C
214D
115C
215F
116C
216G
117C
217H
118C
218I
119D
219F
120D
220G
121D
221H
122D
222I
123F
223G
124F
224H
125F
225I
126G
226H
127G
227I
128H
228I

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASNASNPROPROAA8 - 23328 - 253
21ASNASNPROPROBB8 - 23328 - 253
12ASNASNPROPROAA8 - 23328 - 253
22ASNASNPROPROCC8 - 23328 - 253
13ASNASNPROPROAA8 - 23328 - 253
23ASNASNPROPRODD8 - 23328 - 253
14ASNASNPROPROAA8 - 23328 - 253
24ASNASNPROPROFE8 - 23328 - 253
15ASNASNPROPROAA8 - 23328 - 253
25ASNASNPROPROGF8 - 23328 - 253
16ASNASNLEULEUAA8 - 23228 - 252
26ASNASNLEULEUHG8 - 23228 - 252
17ASNASNLEULEUAA8 - 23228 - 252
27ASNASNLEULEUIH8 - 23228 - 252
18ASNASNPROPROBB8 - 23328 - 253
28ASNASNPROPROCC8 - 23328 - 253
19ASNASNPROPROBB8 - 23328 - 253
29ASNASNPROPRODD8 - 23328 - 253
110ASNASNPROPROBB8 - 23328 - 253
210ASNASNPROPROFE8 - 23328 - 253
111ASNASNPROPROBB8 - 23328 - 253
211ASNASNPROPROGF8 - 23328 - 253
112GLUGLUPROPROBB6 - 23326 - 253
212GLUGLUPROPROHG6 - 23326 - 253
113THRTHRPROPROBB7 - 23327 - 253
213THRTHRPROPROIH7 - 23327 - 253
114ASNASNPROPROCC8 - 23328 - 253
214ASNASNPROPRODD8 - 23328 - 253
115ASNASNPROPROCC8 - 23328 - 253
215ASNASNPROPROFE8 - 23328 - 253
116ASNASNPROPROCC8 - 23328 - 253
216ASNASNPROPROGF8 - 23328 - 253
117ASNASNLEULEUCC8 - 23228 - 252
217ASNASNLEULEUHG8 - 23228 - 252
118ASNASNLEULEUCC8 - 23228 - 252
218ASNASNLEULEUIH8 - 23228 - 252
119ASNASNPROPRODD8 - 23328 - 253
219ASNASNPROPROFE8 - 23328 - 253
120ASNASNPROPRODD8 - 23328 - 253
220ASNASNPROPROGF8 - 23328 - 253
121ASNASNLEULEUDD8 - 23228 - 252
221ASNASNLEULEUHG8 - 23228 - 252
122ASNASNLEULEUDD8 - 23228 - 252
222ASNASNLEULEUIH8 - 23228 - 252
123ASNASNPROPROFE8 - 23328 - 253
223ASNASNPROPROGF8 - 23328 - 253
124ASNASNLEULEUFE8 - 23228 - 252
224ASNASNLEULEUHG8 - 23228 - 252
125ASNASNLEULEUFE8 - 23228 - 252
225ASNASNLEULEUIH8 - 23228 - 252
126ASNASNLEULEUGF8 - 23228 - 252
226ASNASNLEULEUHG8 - 23228 - 252
127ASNASNLEULEUGF8 - 23228 - 252
227ASNASNLEULEUIH8 - 23228 - 252
128THRTHRLEULEUHG7 - 23227 - 252
228THRTHRLEULEUIH7 - 23227 - 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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1445 / 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: 2.41 Å3/Da / Density % sol: 49.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: Sitting drops were set up with 150 nL protein at 13 mg/mL with 150 nL of reservoir: 100 mM citrate buffer at pH 5.5, 12% (w/v) PEG 8000, 20 mM calcium chloride

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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: 1.75→47.8 Å / Num. obs: 223984 / % possible obs: 100 % / Redundancy: 6.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.056 / Net I/σ(I): 9
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.759 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 10986 / CC1/2: 0.847 / Rpim(I) all: 0.546 / % possible all: 100

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Processing

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

6azo


Resolution: 1.75→44.48 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.957 / SU B: 2.539 / SU ML: 0.077 / Cross valid method: THROUGHOUT / ESU R: 0.101 / ESU R Free: 0.099 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20354 11028 5 %RANDOM
Rwork0.17392 ---
obs0.17539 210888 99.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 29.138 Å2
Baniso -1Baniso -2Baniso -3
1-1.56 Å20 Å20 Å2
2--1.3 Å2-0 Å2
3----2.85 Å2
Refinement stepCycle: 1 / Resolution: 1.75→44.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13847 0 31 1445 15323
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.01914462
X-RAY DIFFRACTIONr_bond_other_d0.0020.0213387
X-RAY DIFFRACTIONr_angle_refined_deg1.761.96719657
X-RAY DIFFRACTIONr_angle_other_deg1.069331087
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.59751858
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.55923.606635
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.23152370
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.86415115
X-RAY DIFFRACTIONr_chiral_restr0.120.22143
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02116326
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022870
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_it2.842.7567372
X-RAY DIFFRACTIONr_mcbond_other2.8382.7567371
X-RAY DIFFRACTIONr_mcangle_it3.4554.1149250
X-RAY DIFFRACTIONr_mcangle_other3.4554.1159251
X-RAY DIFFRACTIONr_scbond_it3.6433.0467090
X-RAY DIFFRACTIONr_scbond_other3.5963.0417078
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.0684.44910390
X-RAY DIFFRACTIONr_long_range_B_refined5.86853.42764401
X-RAY DIFFRACTIONr_long_range_B_other5.86853.42864402
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)
11A145980.08
12B145980.08
21A154740.06
22C154740.06
31A153440.06
32D153440.06
41A153480.05
42F153480.05
51A153920.06
52G153920.06
61A152960.06
62H152960.06
71A153000.05
72I153000.05
81B144440.07
82C144440.07
91B145040.07
92D145040.07
101B144660.07
102F144660.07
111B145320.06
112G145320.06
121B146380.07
122H146380.07
131B145340.07
132I145340.07
141C152000.06
142D152000.06
151C152180.06
152F152180.06
161C153320.06
162G153320.06
171C152440.04
172H152440.04
181C151260.06
182I151260.06
191D154440.03
192F154440.03
201D153820.04
202G153820.04
211D152840.06
212H152840.06
221D152580.04
222I152580.04
231F152680.05
232G152680.05
241F152040.06
242H152040.06
251F151740.04
252I151740.04
261G151680.05
262H151680.05
271G151000.06
272I151000.06
281H151240.06
282I151240.06
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 790 -
Rwork0.282 15095 -
obs--96.98 %

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