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- PDB-5hmf: Crystal structure of triazine hydrolase variant (P214T/Y215H/E241Q) -

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Basic information

Entry
Database: PDB / ID: 5hmf
TitleCrystal structure of triazine hydrolase variant (P214T/Y215H/E241Q)
ComponentsTriazine hydrolase
KeywordsHYDROLASE / amidohydrolase
Function / homology
Function and homology information


amidase activity / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds / 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
Triazine hydrolase / Triazine hydrolase
Similarity search - Component
Biological speciesArthrobacter aurescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsSugrue, E. / Carr, P.D. / Jackson, C.J.
CitationJournal: Biochemistry / Year: 2016
Title: Active Site Desolvation and Thermostability Trade-Offs in the Evolution of Catalytically Diverse Triazine Hydrolases.
Authors: Sugrue, E. / Carr, P.D. / Scott, C. / Jackson, C.J.
History
DepositionJan 16, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2016Group: Database references
Revision 1.2Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _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

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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)100,3254
Polymers100,1942
Non-polymers1312
Water14,808822
1
A: Triazine hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,1622
Polymers50,0971
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Triazine hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,1622
Polymers50,0971
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5590 Å2
ΔGint-110 kcal/mol
Surface area29590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.250, 101.670, 80.430
Angle α, β, γ (deg.)90.00, 104.02, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Triazine hydrolase


Mass: 50096.922 Da / Num. of mol.: 2 / Mutation: P216T, Y217H, E243Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrobacter aurescens (bacteria) / Strain: TC1 / Gene: TRZN / Plasmid: petMCSIII / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21
References: UniProt: Q6SJY7, UniProt: A1RCJ9*PLUS, atrazine chlorohydrolase
#2: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 822 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 45.98 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1 M BisTris, 0.1 M Ammonium Acetate, 16% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9501 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 29, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9501 Å / Relative weight: 1
ReflectionResolution: 1.84→55.54 Å / Num. obs: 76523 / % possible obs: 94 % / Redundancy: 3.3 % / Net I/σ(I): 12.8
Reflection shellResolution: 1.84→1.88 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 1.6 / % possible all: 87.5

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
MOSFLMdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LH8

4lh8


Resolution: 1.84→45.965 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1946 3612 5 %
Rwork0.1644 --
obs0.1659 72309 93.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.84→45.965 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6953 0 2 822 7777
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.017212
X-RAY DIFFRACTIONf_angle_d1.2689838
X-RAY DIFFRACTIONf_dihedral_angle_d13.3122619
X-RAY DIFFRACTIONf_chiral_restr0.051103
X-RAY DIFFRACTIONf_plane_restr0.0071307
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.84-1.86420.32361290.27062442X-RAY DIFFRACTION88
1.8642-1.88980.26511290.27892442X-RAY DIFFRACTION86
1.8898-1.91680.33361250.30022412X-RAY DIFFRACTION85
1.9168-1.94540.28731290.27612449X-RAY DIFFRACTION88
1.9454-1.97580.26311320.23362496X-RAY DIFFRACTION88
1.9758-2.00820.24031310.21312507X-RAY DIFFRACTION90
2.0082-2.04280.22281350.20062571X-RAY DIFFRACTION90
2.0428-2.07990.26991310.23332451X-RAY DIFFRACTION88
2.0799-2.11990.21121380.18422596X-RAY DIFFRACTION91
2.1199-2.16320.19531360.1762594X-RAY DIFFRACTION93
2.1632-2.21020.19251360.17672576X-RAY DIFFRACTION92
2.2102-2.26160.24611300.21422598X-RAY DIFFRACTION92
2.2616-2.31820.17851400.16992652X-RAY DIFFRACTION94
2.3182-2.38090.21361420.15712698X-RAY DIFFRACTION95
2.3809-2.45090.20411410.15482665X-RAY DIFFRACTION96
2.4509-2.530.18521430.15082702X-RAY DIFFRACTION96
2.53-2.62050.19131440.15232742X-RAY DIFFRACTION97
2.6205-2.72540.21171440.16152741X-RAY DIFFRACTION97
2.7254-2.84940.17941460.15752763X-RAY DIFFRACTION98
2.8494-2.99960.2031460.16722787X-RAY DIFFRACTION98
2.9996-3.18750.19851470.16142766X-RAY DIFFRACTION98
3.1875-3.43350.19191450.15552783X-RAY DIFFRACTION99
3.4335-3.77890.17321480.13712800X-RAY DIFFRACTION98
3.7789-4.32540.13851480.11772809X-RAY DIFFRACTION99
4.3254-5.44810.13641460.10992815X-RAY DIFFRACTION99
5.4481-45.97950.1561510.13712840X-RAY DIFFRACTION98

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