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- PDB-4gy0: Round 18 Arylesterase Variant of Phosphotriesterase -

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Basic information

Entry
Database: PDB / ID: 4gy0
TitleRound 18 Arylesterase Variant of Phosphotriesterase
Componentsarylesterase variant of phosphotriesterase
KeywordsHYDROLASE / alpha/beta hydrolase / arylesterase
Function / homology
Function and homology information


aryldialkylphosphatase / aryldialkylphosphatase activity / catabolic process / zinc ion binding / plasma membrane
Similarity search - Function
Aryldialkylphosphatase, zinc-binding site / Phosphotriesterase family signature 1. / Phosphotriesterase / Phosphotriesterase family / Phosphotriesterase family profile. / Metal-dependent hydrolases / Metal-dependent hydrolase / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / TIM Barrel ...Aryldialkylphosphatase, zinc-binding site / Phosphotriesterase family signature 1. / Phosphotriesterase / Phosphotriesterase family / Phosphotriesterase family profile. / Metal-dependent hydrolases / Metal-dependent hydrolase / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Biological speciesSynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsJackson, C.J. / Tokuriki, N. / Tawfik, D.S.
CitationJournal: Nat Commun / Year: 2012
Title: Diminishing returns and tradeoffs constrain the laboratory optimization of an enzyme
Authors: Tokuriki, N. / Jackson, C.J. / Afriat-Jurnou, L. / Wyganowski, K.T. / Tang, R. / Tawfik, D.S.
History
DepositionSep 5, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 21, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_alt_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: arylesterase variant of phosphotriesterase
B: arylesterase variant of phosphotriesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,8098
Polymers72,4172
Non-polymers3926
Water8,107450
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3530 Å2
ΔGint-246 kcal/mol
Surface area22670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.109, 86.366, 89.192
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 arylesterase variant of phosphotriesterase


Mass: 36208.414 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synthetic construct (others) / Production host: Escherichia coli (E. coli) / References: UniProt: P0A434*PLUS, aryldialkylphosphatase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 450 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsA SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN IS GENBANK, AFL46607.

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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: 2.29 Å3/Da / Density % sol: 46.29 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 30% MPD, 2% PEG 8K, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Nov 7, 2010
RadiationMonochromator: Si (1 1 1) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 1.85→24.49 Å / Num. all: 57457 / Num. obs: 57457 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 18.69 Å2

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Processing

Software
NameVersionClassification
DNAdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→24.465 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8063 / SU ML: 0.57 / σ(F): 1.35 / Phase error: 25.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2413 2911 5.07 %RANDOM
Rwork0.1948 ---
all0.1972 57457 --
obs0.1972 57408 99.99 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.338 Å2 / ksol: 0.343 e/Å3
Displacement parametersBiso max: 161.92 Å2 / Biso mean: 25.1803 Å2 / Biso min: 4.56 Å2
Baniso -1Baniso -2Baniso -3
1--3.0241 Å20 Å2-0 Å2
2--9.063 Å20 Å2
3----6.039 Å2
Refinement stepCycle: LAST / Resolution: 1.85→24.465 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5000 0 6 450 5456
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085552
X-RAY DIFFRACTIONf_angle_d1.0757597
X-RAY DIFFRACTIONf_chiral_restr0.071892
X-RAY DIFFRACTIONf_plane_restr0.005994
X-RAY DIFFRACTIONf_dihedral_angle_d13.4372071
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 21 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.85-1.88030.34951290.301725532682
1.8803-1.91270.29741480.279725702718
1.9127-1.94750.35041190.257525572676
1.9475-1.98490.3291470.255925492696
1.9849-2.02540.29771450.245125522697
2.0254-2.06950.30211410.237225902731
2.0695-2.11760.2761490.230325322681
2.1176-2.17050.26581360.229425832719
2.1705-2.22910.30091350.225125742709
2.2291-2.29470.30881440.231425602704
2.2947-2.36870.31781570.232325412698
2.3687-2.45330.26031480.212625862734
2.4533-2.55140.28661280.194625982726
2.5514-2.66740.23531320.192825772709
2.6674-2.80780.25921250.179526212746
2.8078-2.98350.20391440.182226002744
2.9835-3.21340.22311140.171226432757
3.2134-3.53590.19141420.171926092751
3.5359-4.04550.18071290.150926512780
4.0455-5.08940.15681520.140926702822
5.0894-24.46670.24831470.192427812928

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