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- PDB-4cqb: The reaction mechanism of the N-isopropylammelide isopropylaminoh... -

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Basic information

Entry
Database: PDB / ID: 4cqb
TitleThe reaction mechanism of the N-isopropylammelide isopropylaminohydrolase AtzC: insights from structural and mutagenesis studies
ComponentsN-ISOPROPYLAMMELIDE ISOPROPYL AMIDOHYDROLASE
KeywordsHYDROLASE / ATRAZINE / ATRAZINE BREAKDOWN
Function / homology
Function and homology information


N-isopropylammelide isopropylaminohydrolase / N-isopropylammelide isopropylaminohydrolase activity / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines / atrazine catabolic process / metal ion binding / cytoplasm
Similarity search - Function
: / Amidohydrolase 3 / Amidohydrolase family / Urease, subunit C; domain 1 / Urease, subunit C, domain 1 / Metal-dependent hydrolase, composite domain superfamily / Metal-dependent hydrolases / Metal-dependent hydrolase / Roll / TIM Barrel ...: / Amidohydrolase 3 / Amidohydrolase family / Urease, subunit C; domain 1 / Urease, subunit C, domain 1 / Metal-dependent hydrolase, composite domain superfamily / Metal-dependent hydrolases / Metal-dependent hydrolase / Roll / TIM Barrel / Alpha-Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
MALONATE ION / N-isopropylammelide isopropyl amidohydrolase
Similarity search - Component
Biological speciesPSEUDOMONAS SP. ADP (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsBalotra, S. / Newman, J. / French, N.G. / Peat, T.S. / Scott, C.
CitationJournal: Plos One / Year: 2015
Title: X-Ray Structure and Mutagenesis Studies of the N-Isopropylammelide Isopropylaminohydrolase, Atzc
Authors: Balotra, S. / Warden, A.C. / Newman, J. / Briggs, L.J. / Scott, C. / Peat, T.S.
History
DepositionFeb 13, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 4, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 30, 2015Group: Database references
Revision 1.2Oct 7, 2015Group: Database references
Revision 1.3Dec 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_asym_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_asym_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: N-ISOPROPYLAMMELIDE ISOPROPYL AMIDOHYDROLASE
B: N-ISOPROPYLAMMELIDE ISOPROPYL AMIDOHYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,08012
Polymers94,3372
Non-polymers74210
Water8,827490
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5640 Å2
ΔGint-100.1 kcal/mol
Surface area27450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.474, 86.733, 114.175
Angle α, β, γ (deg.)90.00, 104.69, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2128-

HOH

21A-2147-

HOH

31B-2010-

HOH

41B-2138-

HOH

51B-2157-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: _ / Auth seq-ID: 4 - 402 / Label seq-ID: 24 - 422

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

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein N-ISOPROPYLAMMELIDE ISOPROPYL AMIDOHYDROLASE


Mass: 47168.660 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS SP. ADP (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: O52063, EC: 3.5.99.4

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Non-polymers , 5 types, 500 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H2O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 490 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsN-TERMINAL HIS-TAG ADDED

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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: 2.86 Å3/Da / Density % sol: 57 % / Description: NONE
Crystal growpH: 7.7
Details: 12 MG/ML PROTEIN WITH A RESERVOIR OF 2.3 M MALONATE AT PH 6.0, 100 MM HEPES PH 7.7; DROPS WERE 200 NL PLUS 200 NL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 23, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.84→46.3 Å / Num. obs: 85852 / % possible obs: 99.3 % / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 10.7
Reflection shellResolution: 1.84→1.94 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 2.7 / % possible all: 95.1

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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 2QT3

2qt3


Resolution: 1.84→40.4 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.919 / SU B: 2.997 / SU ML: 0.092 / Cross valid method: THROUGHOUT / ESU R: 0.129 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.22904 4338 5.1 %RANDOM
Rwork0.19133 ---
obs0.19325 81509 99.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.381 Å2
Baniso -1Baniso -2Baniso -3
1-1.76 Å20 Å20.16 Å2
2---1.27 Å20 Å2
3----0.47 Å2
Refinement stepCycle: LAST / Resolution: 1.84→40.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6291 0 37 490 6818
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0196551
X-RAY DIFFRACTIONr_bond_other_d0.0060.026309
X-RAY DIFFRACTIONr_angle_refined_deg1.7771.9628881
X-RAY DIFFRACTIONr_angle_other_deg1.135314558
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3085826
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.69624.812293
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.858151169
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3931534
X-RAY DIFFRACTIONr_chiral_restr0.120.21011
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.027420
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021414
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_it2.1432.2823271
X-RAY DIFFRACTIONr_mcbond_other2.1432.2813270
X-RAY DIFFRACTIONr_mcangle_it2.6693.8354108
X-RAY DIFFRACTIONr_mcangle_other2.673.8364109
X-RAY DIFFRACTIONr_scbond_it3.3162.6913280
X-RAY DIFFRACTIONr_scbond_other3.3062.6893278
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.644.3354773
X-RAY DIFFRACTIONr_long_range_B_refined5.49312.7247892
X-RAY DIFFRACTIONr_long_range_B_other5.48712.7177890
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 26670 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.06 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.844→1.892 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 285 -
Rwork0.293 5429 -
obs--90.2 %

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