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- PDB-4l9x: Triazine hydrolase from Arthobacter aurescens modified for maximu... -

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Basic information

Entry
Database: PDB / ID: 4l9x
TitleTriazine hydrolase from Arthobacter aurescens modified for maximum expression in E.coli
ComponentsTriazine hydrolase
KeywordsHYDROLASE / amidohydrolase / hydrolases triazine herbicides
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
ACETATE ION / Triazine hydrolase
Similarity search - Component
Biological speciesArthrobacter aurescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsJackson, C.J. / Coppin, C.W. / Alexandrov, A. / Wilding, M. / Liu, J.-W. / Ubels, J. / Paks, M. / Carr, P.D. / Newman, J. / Russell, R.J. ...Jackson, C.J. / Coppin, C.W. / Alexandrov, A. / Wilding, M. / Liu, J.-W. / Ubels, J. / Paks, M. / Carr, P.D. / Newman, J. / Russell, R.J. / Field, M. / Weik, M. / Oakeshott, J.G. / Scott, C.
CitationJournal: Appl.Environ.Microbiol. / Year: 2014
Title: 300-Fold increase in production of the Zn2+-dependent dechlorinase TrzN in soluble form via apoenzyme stabilization.
Authors: Jackson, C.J. / Coppin, C.W. / Carr, P.D. / Aleksandrov, A. / Wilding, M. / Sugrue, E. / Ubels, J. / Paks, M. / Newman, J. / Peat, T.S. / Russell, R.J. / Field, M. / Weik, M. / Oakeshott, J.G. / Scott, C.
History
DepositionJun 18, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 21, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Database references / Derived calculations
Category: citation / database_2 ...citation / database_2 / struct_ref_seq_dif / struct_site
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)102,5503
Polymers102,4912
Non-polymers591
Water10,431579
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5610 Å2
ΔGint-38 kcal/mol
Surface area29680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.110, 101.270, 77.230
Angle α, β, γ (deg.)90.00, 100.98, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: _ / Auth seq-ID: 1 - 453 / Label seq-ID: 14 - 466

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

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Components

#1: Protein Triazine hydrolase


Mass: 51245.262 Da / Num. of mol.: 2 / Mutation: D38N, L131P, A159V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrobacter aurescens (bacteria) / Strain: TC1 / Gene: trzN / Plasmid: pET14b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q6SJY7, atrazine chlorohydrolase
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 579 / 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: 2.1 Å3/Da / Density % sol: 41.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 30% PEG3350, 200mM ammonium sulfate, 100mM Bis-Tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 1.2398 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 12, 2009
Details: undulator, double crystal monochromator, vertical and horizontal mirrors
RadiationMonochromator: Silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2398 Å / Relative weight: 1
ReflectionResolution: 1.85→20 Å / Num. all: 72046 / Num. obs: 72046 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.025 / Net I/σ(I): 14.6
Reflection shellResolution: 1.85→1.95 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.521 / Mean I/σ(I) obs: 2.4 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.7.0032refinement
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3LS9

3ls9


Resolution: 1.85→19.78 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.959 / Cross valid method: THROUGHOUT / ESU R: 0.159 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.19141 3804 5.3 %RANDOM
Rwork0.18844 ---
all0.1886 68412 --
obs0.1886 68057 99.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.375 Å2
Baniso -1Baniso -2Baniso -3
1--1.13 Å20 Å2-1.55 Å2
2--2.18 Å20 Å2
3----0.7 Å2
Refinement stepCycle: LAST / Resolution: 1.85→19.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6987 0 4 579 7570
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0197163
X-RAY DIFFRACTIONr_angle_refined_deg1.1081.9649747
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8035912
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.0622.963324
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.404151128
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3921569
X-RAY DIFFRACTIONr_chiral_restr0.0770.21086
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215537
X-RAY DIFFRACTIONr_mcbond_it2.7772.633652
X-RAY DIFFRACTIONr_mcangle_it3.3493.9254562
X-RAY DIFFRACTIONr_scbond_it4.0632.9153511
X-RAY DIFFRACTIONr_long_range_B_refined5.40523.27511683
Refine LS restraints NCS

Ens-ID: 1 / Number: 563 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.14 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 261 -
Rwork0.292 5022 -
obs--99.44 %

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