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

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Basic information

Entry
Database: PDB / ID: 3lsc
TitleCrystal structure of the mutant E241Q of atrazine chlorohydrolase TrzN from Arthrobacter aurescens TC1 complexed with zinc and atraton
ComponentsTriazine hydrolase
KeywordsHYDROLASE / atrazine chlorohydrolase TrzN / E241Q / atraton
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 ...: / 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-AOO / Triazine hydrolase
Similarity search - Component
Biological speciesArthrobacter aurescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 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 atraton
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)100,0195
Polymers99,6772
Non-polymers3423
Water7,764431
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5500 Å2
ΔGint-72 kcal/mol
Surface area28740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.378, 101.621, 80.767
Angle α, β, γ (deg.)90.00, 104.45, 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-AOO / N-ethyl-6-methoxy-N'-(1-methylethyl)-1,3,5-triazine-2,4-diamine / Atraton


Mass: 211.264 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H17N5O
#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.: 431 / 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: 2.29 Å3/Da / Density % sol: 46.23 %
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: Nov 19, 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: 1.64→40 Å / Num. obs: 108286 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.071

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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: 1.64→39.106 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2143 5408 4.99 %RANDOM
Rwork0.1893 ---
obs0.1906 108286 98.6 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.027 Å2 / ksol: 0.352 e/Å3
Refinement stepCycle: LAST / Resolution: 1.64→39.106 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6956 0 17 431 7404
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067129
X-RAY DIFFRACTIONf_angle_d1.0299699
X-RAY DIFFRACTIONf_dihedral_angle_d15.8972581
X-RAY DIFFRACTIONf_chiral_restr0.0681080
X-RAY DIFFRACTIONf_plane_restr0.0041279
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.64-1.65730.331190.28762628X-RAY DIFFRACTION76
1.6573-1.67680.27081750.28083067X-RAY DIFFRACTION88
1.6768-1.69730.33371670.26493366X-RAY DIFFRACTION96
1.6973-1.71870.28271820.253410X-RAY DIFFRACTION99
1.7187-1.74140.29941610.24653484X-RAY DIFFRACTION100
1.7414-1.76520.27991820.23593461X-RAY DIFFRACTION100
1.7652-1.79040.26541970.22273465X-RAY DIFFRACTION100
1.7904-1.81710.23431830.21823399X-RAY DIFFRACTION100
1.8171-1.84550.25742030.2123501X-RAY DIFFRACTION100
1.8455-1.87580.26121950.20763454X-RAY DIFFRACTION100
1.8758-1.90810.24081820.21033459X-RAY DIFFRACTION100
1.9081-1.94280.26091720.20423467X-RAY DIFFRACTION100
1.9428-1.98020.24591740.19153487X-RAY DIFFRACTION100
1.9802-2.02060.21791580.19073490X-RAY DIFFRACTION100
2.0206-2.06460.22381730.18353492X-RAY DIFFRACTION100
2.0646-2.11260.21521820.18443481X-RAY DIFFRACTION100
2.1126-2.16540.211930.18043451X-RAY DIFFRACTION100
2.1654-2.2240.21411860.18683456X-RAY DIFFRACTION100
2.224-2.28940.21241420.18793535X-RAY DIFFRACTION100
2.2894-2.36330.21651950.18153433X-RAY DIFFRACTION100
2.3633-2.44770.20411870.18893482X-RAY DIFFRACTION100
2.4477-2.54570.22691950.19143466X-RAY DIFFRACTION100
2.5457-2.66150.23152130.19193443X-RAY DIFFRACTION100
2.6615-2.80180.22891910.19773467X-RAY DIFFRACTION100
2.8018-2.97730.20441830.19453496X-RAY DIFFRACTION100
2.9773-3.20710.2212000.20193469X-RAY DIFFRACTION100
3.2071-3.52970.19651910.18993487X-RAY DIFFRACTION100
3.5297-4.040.18361560.15913527X-RAY DIFFRACTION100
4.04-5.08820.15891920.14363508X-RAY DIFFRACTION100
5.0882-39.11710.17471790.16833547X-RAY DIFFRACTION99

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