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- PDB-4bvt: Cyanuric acid hydrolase: evolutionary innovation by structural co... -

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Basic information

Entry
Database: PDB / ID: 4bvt
TitleCyanuric acid hydrolase: evolutionary innovation by structural concatenation
ComponentsCYANURIC ACID AMIDOHYDROLASE
KeywordsHYDROLASE / AMIDASE
Function / homology
Function and homology information


cyanuric acid amidohydrolase / cyanuric acid amidohydrolase activity / atrazine 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
BARBITURIC ACID / DI(HYDROXYETHYL)ETHER / Cyanuric acid amidohydrolase
Similarity search - Component
Biological speciesPSEUDOMONAS SP. ADP (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsPeat, T.S. / Balotra, S. / Wilding, M. / French, N.G. / Briggs, L.J. / Panjikar, S. / Cowieson, N. / Newman, J. / Scott, C.
CitationJournal: Mol.Microbiol. / Year: 2013
Title: Cyanuric Acid Hydrolase: Evolutionary Innovation by Structural Concatenation.
Authors: Peat, T.S. / Balotra, S. / Wilding, M. / French, N.G. / Briggs, L.J. / Panjikar, S. / Cowieson, N. / Newman, J. / Scott, C.
History
DepositionJun 28, 2013Deposition site: PDBE / Processing site: PDBE
SupersessionJul 17, 2013ID: 3ZGU
Revision 1.0Jul 17, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 19, 2017Group: Data collection
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CYANURIC ACID AMIDOHYDROLASE
B: CYANURIC ACID AMIDOHYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,3548
Polymers80,8372
Non-polymers5176
Water1629
1
A: CYANURIC ACID AMIDOHYDROLASE
B: CYANURIC ACID AMIDOHYDROLASE
hetero molecules

A: CYANURIC ACID AMIDOHYDROLASE
B: CYANURIC ACID AMIDOHYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,70916
Polymers161,6754
Non-polymers1,03412
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area12800 Å2
ΔGint-61.2 kcal/mol
Surface area44750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.230, 129.230, 233.791
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: HIS / Beg label comp-ID: HIS / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: _ / Auth seq-ID: 0 - 363 / Label seq-ID: 20 - 383

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

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Components

#1: Protein CYANURIC ACID AMIDOHYDROLASE / CYANURIC ACID HYROLASE


Mass: 40418.656 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS SP. ADP (bacteria) / Strain: ADP
Description: GENE SYNTHESIZED BASED ON SEQUENCE FROM ACCESSION NO U66917
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P58329, cyanuric acid amidohydrolase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-BR8 / BARBITURIC ACID


Mass: 128.086 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H4N2O3
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 2.79 Å3/Da / Density % sol: 55.9 % / Description: NONE
Crystal growpH: 7
Details: THE PROTEIN WAS DIALYSED AGAINST HEPES BUFFER WITH BARBITURIC ACID, THE FINAL CONCENTRATION OF PROTEIN WAS 2 MG/ML AND THIS WAS SET UP IN A 1:1 RATIO AGAINST 180 MM NACL, 31% V/V PEG 400 AND 100 MM HEPES PH 7.0.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 18, 2012 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 3.09→43.1 Å / Num. obs: 13929 / % possible obs: 99.5 % / Observed criterion σ(I): 1 / Redundancy: 9.7 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 12.9
Reflection shellResolution: 3.09→3.26 Å / Redundancy: 9.2 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 3.6 / % possible all: 96.5

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ZGR

3zgr
PDB Unreleased entry


Resolution: 3.1→43.18 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.92 / SU B: 17.921 / SU ML: 0.302 / Cross valid method: THROUGHOUT / ESU R Free: 0.422 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.20891 719 5.2 %RANDOM
Rwork0.16374 ---
obs0.16604 13210 99.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 63.99 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20.08 Å20 Å2
2--0.08 Å20 Å2
3----0.25 Å2
Refinement stepCycle: LAST / Resolution: 3.1→43.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5362 0 34 9 5405
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0195486
X-RAY DIFFRACTIONr_bond_other_d0.0050.025232
X-RAY DIFFRACTIONr_angle_refined_deg1.1441.9587437
X-RAY DIFFRACTIONr_angle_other_deg0.859312016
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3265726
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.81522.694219
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.38515867
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1921549
X-RAY DIFFRACTIONr_chiral_restr0.0530.2858
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0216287
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021202
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_it2.5036.2352910
X-RAY DIFFRACTIONr_mcbond_other2.496.2332909
X-RAY DIFFRACTIONr_mcangle_it4.1189.3483634
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.7876.7072576
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 21824 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.09 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 3.095→3.176 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 46 -
Rwork0.255 910 -
obs--93 %

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