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- PDB-4xd3: Phosphotriesterase variant E3 -

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Basic information

Entry
Database: PDB / ID: 4xd3
TitlePhosphotriesterase variant E3
ComponentsPhosphotriesterase variant PTE-E1
KeywordsHYDROLASE / dynamics / evolution / phosphotriesterase
Function / homology
Function and homology information


catabolic process / hydrolase activity, acting on ester bonds / 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-E1
Similarity search - Component
Biological speciesBrevundimonas diminuta (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 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 19, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2015Provider: repository / Type: Initial release
Revision 1.1May 11, 2016Group: Structure summary
Revision 1.2Sep 7, 2016Group: Database references
Revision 1.3Sep 28, 2016Group: Database references
Revision 1.4Oct 26, 2016Group: Database references
Revision 1.5Sep 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 1.6Nov 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-E1
G: Phosphotriesterase variant PTE-E1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,29112
Polymers72,2832
Non-polymers1,00810
Water12,106672
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4720 Å2
ΔGint-179 kcal/mol
Surface area22350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.830, 85.882, 88.721
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11G-581-

HOH

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Components

#1: Protein Phosphotriesterase variant PTE-E1


Mass: 36141.258 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: A0A060GPQ5
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate / Cacodylic acid


Mass: 136.989 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6AsO2
#4: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 672 / 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: 2.26 Å3/Da / Density % sol: 45.62 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / Details: 100 mM NaCacodylate 30% 2-methane-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, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.57→39.41 Å / Num. obs: 91982 / % possible obs: 99.91 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.0828 / Net I/σ(I): 16.45
Reflection shellResolution: 1.57→1.626 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.9643 / Mean I/σ(I) obs: 2.31 / % possible all: 99.94

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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: 1.57→39.408 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2017 4486 4.88 %
Rwork0.1738 --
obs0.1751 91957 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.57→39.408 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5010 0 46 672 5728
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075269
X-RAY DIFFRACTIONf_angle_d1.1437176
X-RAY DIFFRACTIONf_dihedral_angle_d13.8521921
X-RAY DIFFRACTIONf_chiral_restr0.044834
X-RAY DIFFRACTIONf_plane_restr0.006930
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.57-1.58780.31721520.25532876X-RAY DIFFRACTION100
1.5878-1.60650.27161640.24972861X-RAY DIFFRACTION100
1.6065-1.62610.30491770.24282849X-RAY DIFFRACTION100
1.6261-1.64670.25991540.24322877X-RAY DIFFRACTION100
1.6467-1.66840.25891540.23352902X-RAY DIFFRACTION100
1.6684-1.69120.25991400.22722891X-RAY DIFFRACTION100
1.6912-1.71540.26481640.22652858X-RAY DIFFRACTION100
1.7154-1.7410.2181260.22362898X-RAY DIFFRACTION100
1.741-1.76820.26131510.21132878X-RAY DIFFRACTION100
1.7682-1.79720.23391400.2152885X-RAY DIFFRACTION100
1.7972-1.82820.25871380.20782916X-RAY DIFFRACTION100
1.8282-1.86140.24811690.20262864X-RAY DIFFRACTION100
1.8614-1.89720.23791530.19662902X-RAY DIFFRACTION100
1.8972-1.93590.22351360.19312882X-RAY DIFFRACTION100
1.9359-1.9780.2171300.18812930X-RAY DIFFRACTION100
1.978-2.0240.24141280.18582911X-RAY DIFFRACTION100
2.024-2.07470.20091640.17832879X-RAY DIFFRACTION100
2.0747-2.13080.221460.18322928X-RAY DIFFRACTION100
2.1308-2.19340.19781220.17472908X-RAY DIFFRACTION100
2.1934-2.26420.20451170.16912948X-RAY DIFFRACTION100
2.2642-2.34520.2171710.17142887X-RAY DIFFRACTION100
2.3452-2.4390.18291240.16612950X-RAY DIFFRACTION100
2.439-2.550.19511700.17292894X-RAY DIFFRACTION100
2.55-2.68440.22541570.16932969X-RAY DIFFRACTION100
2.6844-2.85260.19941240.16222921X-RAY DIFFRACTION100
2.8526-3.07280.19841530.16792967X-RAY DIFFRACTION100
3.0728-3.38180.18281810.15872896X-RAY DIFFRACTION100
3.3818-3.87080.16851970.1462956X-RAY DIFFRACTION100
3.8708-4.87540.15171520.13223013X-RAY DIFFRACTION100
4.8754-39.42060.16721320.16493175X-RAY DIFFRACTION100

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