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

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Basic information

Entry
Database: PDB / ID: 6azo
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 / SAD / Resolution: 2.46 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 1.1Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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)116,3626
Polymers116,2914
Non-polymers712
Water7,440413
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12170 Å2
ΔGint-43 kcal/mol
Surface area29060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.688, 100.957, 65.605
Angle α, β, γ (deg.)90.00, 91.84, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROAA8 - 23728 - 257
21PROPROBB8 - 23728 - 257
12VALVALAA8 - 23628 - 256
22VALVALCC8 - 23628 - 256
13PROPROAA8 - 23728 - 257
23PROPRODD8 - 23728 - 257
14VALVALBB8 - 23628 - 256
24VALVALCC8 - 23628 - 256
15PROPROBB8 - 23728 - 257
25PROPRODD8 - 23728 - 257
16VALVALCC8 - 23628 - 256
26VALVALDD8 - 23628 - 256

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Putative amidase


Mass: 29072.729 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-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 413 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.96 Å3/Da / Density % sol: 37.23 %
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop / pH: 6.1
Details: Protein at 4 mg/mL was set up in 200 nL plus 200 nL drops with reservoir: 100 mM bis-tris chloride at pH 6.1, 20.7% (w/v) PEG 4000, 89 mM lithium sulfate at 8C

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.97919 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 30, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97919 Å / Relative weight: 1
ReflectionResolution: 2.46→47.9 Å / Num. obs: 32094 / % possible obs: 99.7 % / Redundancy: 19.8 % / CC1/2: 0.991 / Rpim(I) all: 0.066 / Net I/σ(I): 11.4
Reflection shellResolution: 2.46→2.56 Å / Redundancy: 7.4 % / Mean I/σ(I) obs: 2.7 / Num. unique obs: 3560 / CC1/2: 0.817 / Rpim(I) all: 0.307 / % possible all: 98

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
Aimlessdata scaling
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 2.46→44.99 Å / Cor.coef. Fo:Fc: 0.894 / Cor.coef. Fo:Fc free: 0.83 / SU B: 12.347 / SU ML: 0.268 / Cross valid method: THROUGHOUT / ESU R: 1.997 / ESU R Free: 0.342 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27603 1647 5.1 %RANDOM
Rwork0.22525 ---
obs0.22789 30444 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 17.304 Å2
Baniso -1Baniso -2Baniso -3
1-1.78 Å20 Å20.02 Å2
2---0.55 Å2-0 Å2
3----1.23 Å2
Refinement stepCycle: 1 / Resolution: 2.46→44.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7038 0 2 413 7453
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0197203
X-RAY DIFFRACTIONr_bond_other_d0.0020.026727
X-RAY DIFFRACTIONr_angle_refined_deg1.6341.9819775
X-RAY DIFFRACTIONr_angle_other_deg1.077315607
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0825918
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.56823.645310
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.873151109
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0131556
X-RAY DIFFRACTIONr_chiral_restr0.0980.21077
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0218048
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021408
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_it0.8621.7733683
X-RAY DIFFRACTIONr_mcbond_other0.861.7713682
X-RAY DIFFRACTIONr_mcangle_it1.4742.6524597
X-RAY DIFFRACTIONr_mcangle_other1.4742.6534598
X-RAY DIFFRACTIONr_scbond_it0.8511.83520
X-RAY DIFFRACTIONr_scbond_other0.8511.8013521
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.4232.6855179
X-RAY DIFFRACTIONr_long_range_B_refined3.62132.90131828
X-RAY DIFFRACTIONr_long_range_B_other3.5733.02531533
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)
11A152420.07
12B152420.07
21A151760.07
22C151760.07
31A152920.06
32D152920.06
41B154520.05
42C154520.05
51B151800.07
52D151800.07
61C151940.07
62D151940.07
LS refinement shellResolution: 2.46→2.524 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 114 -
Rwork0.289 2188 -
obs--97.3 %

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