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- PDB-5akq: X-ray structure and mutagenesis studies of the N-isopropylammelid... -

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Basic information

Entry
Database: PDB / ID: 5akq
TitleX-ray structure and mutagenesis studies of the N-isopropylammelide isopropylaminohydrolase, AtzC
ComponentsN-ISOPROPYLAMMELIDE ISOPROPYL AMIDOHYDROLASE
KeywordsHYDROLASE / ATRAZINE DEGRADATION / ENZYME EVOLUTION
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: 2.6 Å
AuthorsBalotra, S. / Warden, A.C. / Newman, J. / Briggs, L.J. / Scott, C. / Peat, T.S.
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
DepositionMar 5, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 18, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 30, 2015Group: Database references
Revision 1.2Oct 7, 2015Group: Database references
Revision 1.3Jan 10, 2024Group: 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)94,5416
Polymers94,3392
Non-polymers2024
Water61334
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4000 Å2
ΔGint-89.5 kcal/mol
Surface area27620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.204, 86.581, 114.066
Angle α, β, γ (deg.)90.00, 104.36, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1404-

CL

21B-1404-

CL

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Components

#1: Protein N-ISOPROPYLAMMELIDE ISOPROPYL AMIDOHYDROLASE


Mass: 47169.645 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: N-TERMINAL HIS-TAG WITH THROMBIN CLEAVAGE SITE ADDED TO THE FULL LENGTH ENZYME WITH THE N304D MUTATION
Source: (gene. exp.) PSEUDOMONAS SP. ADP (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O52063, EC: 3.5.99.4
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 2.85 Å3/Da / Density % sol: 56.9 % / Description: NONE
Crystal growpH: 7
Details: 4.0 MG/ML PROTEIN; RESERVOIR WAS 2.56 M MALONATE AT PH 7.0; 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: Apr 3, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.6→46.2 Å / Num. obs: 30950 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Rmerge(I) obs: 0.26 / Net I/σ(I): 6.9
Reflection shellResolution: 2.6→2.72 Å / Redundancy: 7.4 % / Rmerge(I) obs: 1.04 / Mean I/σ(I) obs: 2.1 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4CQB

4cqb


Resolution: 2.6→110.5 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.897 / SU B: 28.761 / SU ML: 0.262 / Cross valid method: THROUGHOUT / ESU R: 0.666 / ESU R Free: 0.296 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.24129 1525 4.9 %RANDOM
Rwork0.20451 ---
obs0.20637 29424 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.038 Å2
Baniso -1Baniso -2Baniso -3
1-0.83 Å20 Å20.19 Å2
2---2.72 Å20 Å2
3---1.58 Å2
Refinement stepCycle: LAST / Resolution: 2.6→110.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6276 0 4 34 6314
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0196392
X-RAY DIFFRACTIONr_bond_other_d0.0080.026176
X-RAY DIFFRACTIONr_angle_refined_deg1.7221.9598652
X-RAY DIFFRACTIONr_angle_other_deg1.423314240
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3925798
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.75624.685286
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.662151146
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7131534
X-RAY DIFFRACTIONr_chiral_restr0.1010.2988
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.027168
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021382
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_it2.0942.8333198
X-RAY DIFFRACTIONr_mcbond_other2.0922.8323197
X-RAY DIFFRACTIONr_mcangle_it3.3164.2463994
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.7043.1743194
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: 2.6→2.668 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 107 -
Rwork0.304 2150 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: -13.9812 Å / Origin y: 22.3125 Å / Origin z: 29.1989 Å
111213212223313233
T0.0803 Å20.0217 Å20.0061 Å2-0.0334 Å20.0054 Å2--0.0136 Å2
L0.0283 °20.0017 °20.0148 °2-0.1653 °20.0247 °2--0.3978 °2
S-0.0095 Å °0.0191 Å °0.0107 Å °-0.02 Å °-0.0492 Å °0.0153 Å °0.005 Å °0.002 Å °0.0587 Å °

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