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

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Basic information

Entry
Database: PDB / ID: 4cqc
TitleThe reaction mechanism of the N-isopropylammelide isopropylaminohydrolase AtzC: insights from structural and mutagenesis studies
ComponentsN-ISOPROPYLAMMELIDE ISOPROPYL AMIDOHYDROLASE
KeywordsHYDROLASE / 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
N-isopropylammelide isopropyl amidohydrolase
Similarity search - Component
Biological speciesPSEUDOMONAS SP. ADP (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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_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_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)94,8828
Polymers94,2032
Non-polymers6786
Water3,351186
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4200 Å2
ΔGint-91.6 kcal/mol
Surface area28780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.234, 87.280, 114.364
Angle α, β, γ (deg.)90.00, 103.93, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1405-

CL

21B-1405-

CL

31A-2040-

HOH

41B-2054-

HOH

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Components

#1: Protein N-ISOPROPYLAMMELIDE ISOPROPYL AMIDOHYDROLASE


Mass: 47101.590 Da / Num. of mol.: 2 / Mutation: YES
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
#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-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsN-TERMINAL HIS-TAG PLUS ONE MUTATION AT POSITION 219

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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: 2.89 Å3/Da / Density % sol: 57.5 % / Description: NONE
Crystal growpH: 7.5
Details: PROTEIN AT 5.5 MG/ML OVER A RESERVOIR OF 2.5 M MALONATE PH 7.0, 100 MM HEPES BUFFER AT PH 7.5; DROPS WERE 150 NL PLUS 150 NL. IN-SITU THROMBIN TREATMENT WAS USED TO REMOVE THE HIS-TAG.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 1.008
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 14, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.008 Å / Relative weight: 1
ReflectionResolution: 2.2→46.3 Å / Num. obs: 51202 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 7.7 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 12.5
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 2.8 / % possible all: 98.9

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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: 2.2→46.37 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.931 / SU B: 5.264 / SU ML: 0.133 / Cross valid method: THROUGHOUT / ESU R: 0.237 / ESU R Free: 0.184 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.22311 2603 5.1 %RANDOM
Rwork0.19556 ---
obs0.19695 48598 99.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.228 Å2
Baniso -1Baniso -2Baniso -3
1-2.59 Å20 Å20.43 Å2
2---2.77 Å20 Å2
3---0.06 Å2
Refinement stepCycle: LAST / Resolution: 2.2→46.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6275 0 34 186 6495
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0196474
X-RAY DIFFRACTIONr_bond_other_d0.0020.026249
X-RAY DIFFRACTIONr_angle_refined_deg1.2691.9648771
X-RAY DIFFRACTIONr_angle_other_deg0.824314424
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9165811
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.2124.81289
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.926151157
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8521534
X-RAY DIFFRACTIONr_chiral_restr0.0740.2995
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.027287
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021391
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_it2.3383.9593232
X-RAY DIFFRACTIONr_mcbond_other2.3383.9593231
X-RAY DIFFRACTIONr_mcangle_it3.3216.6634047
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.1274.5273242
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
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 188 -
Rwork0.259 3523 -
obs--98.64 %

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