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- PDB-3lsb: Crystal structure of the mutant E241Q of atrazine chlorohydrolase... -

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Basic information

Entry
Database: PDB / ID: 3lsb
TitleCrystal structure of the mutant E241Q of atrazine chlorohydrolase TrzN from Arthrobacter aurescens TC1 complexed with zinc and ametrin
ComponentsTriazine hydrolase
KeywordsHYDROLASE / TRZN / E241Q / ametrin
Function / homology
Function and homology information


amidase activity / metal ion binding
Similarity search - Function
Urease, subunit C; domain 1 / Urease, subunit C, domain 1 / Amidohydrolase family / Metal-dependent hydrolase, composite domain superfamily / Amidohydrolase-related / Metal-dependent hydrolases / Metal-dependent hydrolase / Roll / TIM Barrel / Alpha-Beta Barrel ...Urease, subunit C; domain 1 / Urease, subunit C, domain 1 / Amidohydrolase family / Metal-dependent hydrolase, composite domain superfamily / Amidohydrolase-related / Metal-dependent hydrolases / Metal-dependent hydrolase / Roll / TIM Barrel / Alpha-Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-RYN / Triazine hydrolase
Similarity search - Component
Biological speciesArthrobacter aurescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.932 Å
AuthorsFedorov, A.A. / Fedorov, E.V. / Seffernick, J. / Wackett, L.P. / Almo, S.C.
CitationJournal: To be Published
Title: Crystal structure of the mutant E241Q of atrazine chlorohydrolase TrzN from Arthrobacter aurescens TC1 complexed with zinc and Ametryn
Authors: Fedorov, A.A. / Fedorov, E.V. / Seffernick, J. / Wackett, L.P. / Almo, S.C.
History
DepositionFeb 12, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 21, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Triazine hydrolase
B: Triazine hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,0355
Polymers99,6772
Non-polymers3583
Water3,405189
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5510 Å2
ΔGint-71 kcal/mol
Surface area28660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.398, 100.845, 80.635
Angle α, β, γ (deg.)90.00, 104.42, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Triazine hydrolase


Mass: 49838.668 Da / Num. of mol.: 2 / Fragment: UNP residues 14-469 / Mutation: E241Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrobacter aurescens (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q6SJY7
#2: Chemical ChemComp-RYN / N-ethyl-N'-(1-methylethyl)-6-(methylsulfanyl)-1,3,5-triazine-2,4-diamine / Ametryn


Mass: 227.330 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H17N5S
#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.: 189 / 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: 2.27 Å3/Da / Density % sol: 45.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 30% PEG4000, 0.1M Sodium citrate, 0.2M ammonium acetate , pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 22, 2009
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.932→40 Å / Num. obs: 65334 / % possible obs: 98.14 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.066

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
BALBESphasing
PHENIX(phenix.refine: 1.5_2)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDb entry 3LS9

3ls9


Resolution: 1.932→39.047 Å / SU ML: 0.24 / Isotropic thermal model: RANDOM / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2282 3311 5.07 %
Rwork0.1908 --
obs0.1927 65334 98.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.123 Å2 / ksol: 0.365 e/Å3
Refinement stepCycle: LAST / Resolution: 1.932→39.047 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6956 0 17 189 7162
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067129
X-RAY DIFFRACTIONf_angle_d0.9929699
X-RAY DIFFRACTIONf_dihedral_angle_d16.3672583
X-RAY DIFFRACTIONf_chiral_restr0.0671080
X-RAY DIFFRACTIONf_plane_restr0.0051279
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.932-1.95970.351050.33622038X-RAY DIFFRACTION77
1.9597-1.9890.3711210.30872404X-RAY DIFFRACTION92
1.989-2.02010.32631360.29012495X-RAY DIFFRACTION95
2.0201-2.05320.35031260.27682594X-RAY DIFFRACTION98
2.0532-2.08860.33971490.28412524X-RAY DIFFRACTION97
2.0886-2.12660.3221280.24192626X-RAY DIFFRACTION99
2.1266-2.16750.28291330.21572595X-RAY DIFFRACTION100
2.1675-2.21170.30111610.22112605X-RAY DIFFRACTION100
2.2117-2.25980.3171460.25032606X-RAY DIFFRACTION99
2.2598-2.31240.24251240.22172628X-RAY DIFFRACTION100
2.3124-2.37020.2881220.2152650X-RAY DIFFRACTION100
2.3702-2.43420.25211280.20232634X-RAY DIFFRACTION100
2.4342-2.50590.26381400.20092637X-RAY DIFFRACTION100
2.5059-2.58670.2651520.19742592X-RAY DIFFRACTION100
2.5867-2.67920.25941560.21082614X-RAY DIFFRACTION100
2.6792-2.78640.25081450.1962634X-RAY DIFFRACTION100
2.7864-2.91320.25421390.1992616X-RAY DIFFRACTION100
2.9132-3.06670.23841380.20242652X-RAY DIFFRACTION100
3.0667-3.25880.23971410.19282612X-RAY DIFFRACTION100
3.2588-3.51020.22721440.1842658X-RAY DIFFRACTION100
3.5102-3.86320.20321590.16582622X-RAY DIFFRACTION100
3.8632-4.42150.14211350.14642654X-RAY DIFFRACTION100
4.4215-5.56810.17271400.14892645X-RAY DIFFRACTION100
5.5681-39.05530.18491430.16322688X-RAY DIFFRACTION99

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