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- PDB-4xag: Cycles of destabilization and repair underlie the evolution of ne... -

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Basic information

Entry
Database: PDB / ID: 4xag
TitleCycles of destabilization and repair underlie the evolution of new enzyme function
ComponentsPhosphotriesterase variant PTE-R6
KeywordsHYDROLASE / dynamics / evolution / phosphotriesterase
Function / homology
Function and homology information


hydrolase activity, acting on ester bonds / catabolic process / zinc ion binding
Similarity search - Function
Aryldialkylphosphatase, zinc-binding site / Phosphotriesterase family signature 1. / Phosphotriesterase / Phosphotriesterase family / Phosphotriesterase family profile. / Metal-dependent hydrolases / Metal-dependent hydrolase / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
CACODYLATE ION / Phosphotriesterase variant PTE-R6
Similarity search - Component
Biological speciesBrevundimonas diminuta (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsJackson, C.J. / Campbell, E. / Kaltenbach, M. / Tokuriki, N.
CitationJournal: Nat.Chem.Biol. / Year: 2016
Title: The role of protein dynamics in the evolution of new enzyme function.
Authors: Campbell, E. / Kaltenbach, M. / Correy, G.J. / Carr, P.D. / Porebski, B.T. / Livingstone, E.K. / Afriat-Jurnou, L. / Buckle, A.M. / Weik, M. / Hollfelder, F. / Tokuriki, N. / Jackson, C.J.
History
DepositionDec 14, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 7, 2016Group: Database references
Revision 1.2Sep 28, 2016Group: Database references
Revision 1.3Oct 26, 2016Group: Database references
Revision 1.4Sep 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 / pdbx_struct_oper_list / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_id / _struct_conn_type.id
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phosphotriesterase variant PTE-R6
G: Phosphotriesterase variant PTE-R6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,98211
Polymers72,1102
Non-polymers8719
Water8,431468
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3870 Å2
ΔGint-158 kcal/mol
Surface area22720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.886, 86.304, 88.583
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Phosphotriesterase variant PTE-R6


Mass: 36055.188 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brevundimonas diminuta (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A060GPQ0
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6AsO2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 468 / 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: 2.28 Å3/Da / Density % sol: 45.97 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / Details: 100 mM cacodylate, 30% 2-methyl-2,4-pentanediol / PH range: 6-7

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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: Apr 18, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.6→39.41 Å / Num. obs: 87372 / % possible obs: 99.98 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.1212 / Net I/σ(I): 14.24

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GY0

4gy0


Resolution: 1.6→39.405 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2021 4381 5.01 %
Rwork0.164 --
obs0.1659 87362 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→39.405 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5010 0 41 468 5519
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0185433
X-RAY DIFFRACTIONf_angle_d1.7797428
X-RAY DIFFRACTIONf_dihedral_angle_d14.0552008
X-RAY DIFFRACTIONf_chiral_restr0.092872
X-RAY DIFFRACTIONf_plane_restr0.009969
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.61820.30411430.24512731X-RAY DIFFRACTION100
1.6182-1.63720.27621330.2342733X-RAY DIFFRACTION100
1.6372-1.65720.28431580.23852732X-RAY DIFFRACTION100
1.6572-1.67820.26971450.22682712X-RAY DIFFRACTION100
1.6782-1.70020.24461520.21842740X-RAY DIFFRACTION100
1.7002-1.72350.24861540.22082711X-RAY DIFFRACTION100
1.7235-1.74820.2721480.2122745X-RAY DIFFRACTION100
1.7482-1.77430.22331250.19562761X-RAY DIFFRACTION100
1.7743-1.8020.24261460.19662719X-RAY DIFFRACTION100
1.802-1.83150.23131540.19122738X-RAY DIFFRACTION100
1.8315-1.86310.22671280.1782753X-RAY DIFFRACTION100
1.8631-1.8970.2281530.18092748X-RAY DIFFRACTION100
1.897-1.93350.21061400.17642760X-RAY DIFFRACTION100
1.9335-1.97290.22221330.17712733X-RAY DIFFRACTION100
1.9729-2.01580.22781440.16932761X-RAY DIFFRACTION100
2.0158-2.06270.23061490.16632767X-RAY DIFFRACTION100
2.0627-2.11430.2111500.17432729X-RAY DIFFRACTION100
2.1143-2.17150.1761470.15672764X-RAY DIFFRACTION100
2.1715-2.23540.18791580.15522734X-RAY DIFFRACTION100
2.2354-2.30750.19941370.14982758X-RAY DIFFRACTION100
2.3075-2.390.15171570.14922778X-RAY DIFFRACTION100
2.39-2.48560.17431420.15182749X-RAY DIFFRACTION100
2.4856-2.59870.1861630.15062766X-RAY DIFFRACTION100
2.5987-2.73570.19481420.15052777X-RAY DIFFRACTION100
2.7357-2.90710.18921240.15262815X-RAY DIFFRACTION100
2.9071-3.13140.20531460.15632793X-RAY DIFFRACTION100
3.1314-3.44640.21021280.15352843X-RAY DIFFRACTION100
3.4464-3.94470.16481500.14252813X-RAY DIFFRACTION100
3.9447-4.96840.16061750.13662830X-RAY DIFFRACTION100
4.9684-39.41720.22171570.16592988X-RAY DIFFRACTION100

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