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- PDB-5hme: Crystal structure of Triazine Hydrolase variant (P214T/Y215H) -

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Basic information

Entry
Database: PDB / ID: 5hme
TitleCrystal structure of Triazine Hydrolase variant (P214T/Y215H)
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 / 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
Triazine hydrolase / Triazine hydrolase
Similarity search - Component
Biological speciesArthrobacter aurescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.151 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)100,3274
Polymers100,1962
Non-polymers1312
Water8,305461
1
A: Triazine hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,1632
Polymers50,0981
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Triazine hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,1632
Polymers50,0981
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 area5610 Å2
ΔGint-111 kcal/mol
Surface area29960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.551, 100.718, 78.851
Angle α, β, γ (deg.)90.00, 102.30, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Triazine hydrolase


Mass: 50097.906 Da / Num. of mol.: 2 / Mutation: P216T, Y217H
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 / Water


Mass: 18.015 Da / Num. of mol.: 461 / 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: 2.2 Å3/Da / Density % sol: 44.16 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1 M Bis Tris, 0.1M Ammonium Acetate, 16% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 26, 2015
RadiationMonochromator: Silicon Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.15→35.98 Å / Num. obs: 46881 / % possible obs: 99.7 % / Redundancy: 6.4 % / Net I/σ(I): 7.3
Reflection shellResolution: 2.15→2.23 Å / Redundancy: 6.4 % / Mean I/σ(I) obs: 2.3 / % possible all: 98.5

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LH8
Resolution: 2.151→35.979 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2266 2328 4.99 %
Rwork0.2033 --
obs0.2045 46686 99.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.151→35.979 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6953 0 2 461 7416
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0157161
X-RAY DIFFRACTIONf_angle_d1.4869760
X-RAY DIFFRACTIONf_dihedral_angle_d13.8622595
X-RAY DIFFRACTIONf_chiral_restr0.0691095
X-RAY DIFFRACTIONf_plane_restr0.0081293
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1507-2.19460.38651270.34882577X-RAY DIFFRACTION97
2.1946-2.24230.3611480.32852580X-RAY DIFFRACTION100
2.2423-2.29440.33631490.31722587X-RAY DIFFRACTION100
2.2944-2.35180.3381550.28162572X-RAY DIFFRACTION99
2.3518-2.41540.3441230.27242599X-RAY DIFFRACTION99
2.4154-2.48640.27941320.26722613X-RAY DIFFRACTION100
2.4864-2.56670.26191170.24982647X-RAY DIFFRACTION100
2.5667-2.65840.29531260.23852597X-RAY DIFFRACTION99
2.6584-2.76480.27681420.23792584X-RAY DIFFRACTION100
2.7648-2.89060.2991350.23092637X-RAY DIFFRACTION100
2.8906-3.04290.24381270.22842622X-RAY DIFFRACTION100
3.0429-3.23340.23311210.21022609X-RAY DIFFRACTION100
3.2334-3.48290.21041460.18512612X-RAY DIFFRACTION100
3.4829-3.8330.18361480.16032587X-RAY DIFFRACTION100
3.833-4.38680.17441380.1382654X-RAY DIFFRACTION100
4.3868-5.52370.14841470.13152608X-RAY DIFFRACTION99
5.5237-35.98430.14971470.1582673X-RAY DIFFRACTION100

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