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

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Basic information

Entry
Database: PDB / ID: 5hmd
TitleCrystal structure of triazine hydrolase variant (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 / 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: 2.1 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)100,3174
Polymers100,1862
Non-polymers1312
Water8,647480
1
A: Triazine hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,1582
Polymers50,0931
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Triazine hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,1582
Polymers50,0931
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 area5560 Å2
ΔGint-112 kcal/mol
Surface area29480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.154, 99.415, 77.183
Angle α, β, γ (deg.)90.00, 101.12, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Triazine hydrolase


Mass: 50092.934 Da / Num. of mol.: 2
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.: 480 / 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: 2.12 Å3/Da / Density % sol: 41.97 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1M Bis Tris, 0.1M Ammonium acetate, 16% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 2, 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: 2.1→19.69 Å / Num. obs: 47950 / % possible obs: 98.6 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.131 / Net I/σ(I): 11.1
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.557 / Mean I/σ(I) obs: 2.7 / % possible all: 93.3

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LH8
Resolution: 2.1→19.685 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2029 2396 5 %
Rwork0.1453 --
obs0.1482 47916 98.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→19.685 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6953 0 2 480 7435
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0137182
X-RAY DIFFRACTIONf_angle_d1.4639792
X-RAY DIFFRACTIONf_dihedral_angle_d13.7062609
X-RAY DIFFRACTIONf_chiral_restr0.0661095
X-RAY DIFFRACTIONf_plane_restr0.0091300
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0986-2.14130.2661310.21052477X-RAY DIFFRACTION91
2.1413-2.18790.24841370.20242619X-RAY DIFFRACTION98
2.1879-2.23870.25071420.19922703X-RAY DIFFRACTION98
2.2387-2.29460.29281410.18312653X-RAY DIFFRACTION99
2.2946-2.35650.25521400.18072674X-RAY DIFFRACTION99
2.3565-2.42570.25171410.16942680X-RAY DIFFRACTION99
2.4257-2.50390.21841390.1662650X-RAY DIFFRACTION99
2.5039-2.59320.23291420.15842691X-RAY DIFFRACTION99
2.5932-2.69680.21471410.16052686X-RAY DIFFRACTION99
2.6968-2.81920.24591420.15772685X-RAY DIFFRACTION99
2.8192-2.96730.24551410.15752706X-RAY DIFFRACTION99
2.9673-3.15250.20441430.14822682X-RAY DIFFRACTION99
3.1525-3.39480.17411410.14122693X-RAY DIFFRACTION99
3.3948-3.73430.1671430.11842724X-RAY DIFFRACTION99
3.7343-4.26990.16731440.10932717X-RAY DIFFRACTION100
4.2699-5.36160.15081430.10662717X-RAY DIFFRACTION100
5.3616-19.68620.16761450.12842763X-RAY DIFFRACTION99

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