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- PDB-4gy1: Round 18 Arylesterase Variant of Phosphotriesterase with Bound Ca... -

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Basic information

Entry
Database: PDB / ID: 4gy1
TitleRound 18 Arylesterase Variant of Phosphotriesterase with Bound Cacodylate
Componentsarylesterase variant of phosphotriesterase
KeywordsHYDROLASE / alpha/beta hydrolase / arylesterase / carboxylated lysine
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
CACODYLATE ION / Parathion hydrolase
Similarity search - Component
Biological speciesSynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)73,16910
Polymers72,5032
Non-polymers6668
Water10,431579
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4090 Å2
ΔGint-237 kcal/mol
Surface area22560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.223, 87.019, 88.939
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: 36251.414 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: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6AsO2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 579 / 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: 2.3 Å3/Da / Density % sol: 46.54 %
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: ID14-4 / Wavelength: 0.9395 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 12, 2009
RadiationMonochromator: Si (1 1 1) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9395 Å / Relative weight: 1
ReflectionResolution: 1.5→44.47 Å / Num. all: 107473 / Num. obs: 107366 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 14.82 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: 1.5→39.598 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8549 / SU ML: 0.36 / σ(F): 1.34 / Phase error: 21.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2149 5353 4.99 %RANDOM
Rwork0.1941 ---
all0.1951 107366 --
obs0.1951 107280 99.8 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.676 Å2 / ksol: 0.324 e/Å3
Displacement parametersBiso max: 76.97 Å2 / Biso mean: 19.2813 Å2 / Biso min: 6.36 Å2
Baniso -1Baniso -2Baniso -3
1--0.9311 Å20 Å2-0 Å2
2--4.894 Å20 Å2
3----3.9629 Å2
Refinement stepCycle: LAST / Resolution: 1.5→39.598 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5039 0 16 579 5634
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076927
X-RAY DIFFRACTIONf_angle_d1.1289625
X-RAY DIFFRACTIONf_chiral_restr0.071138
X-RAY DIFFRACTIONf_plane_restr0.0061275
X-RAY DIFFRACTIONf_dihedral_angle_d13.3072656
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5-1.5170.28241670.26763341350899
1.517-1.53490.29741580.255633683526100
1.5349-1.55360.28351850.261333623547100
1.5536-1.57330.28581630.2533463509100
1.5733-1.5940.25221750.235533873562100
1.594-1.61580.2741940.225833393533100
1.6158-1.63890.24831950.227433183513100
1.6389-1.66340.26081640.229833863550100
1.6634-1.68940.23441850.219633783563100
1.6894-1.71710.23521720.217833793551100
1.7171-1.74670.24711690.217733703539100
1.7467-1.77840.2341660.210434113577100
1.7784-1.81260.26011700.205933553525100
1.8126-1.84960.23321910.209933983589100
1.8496-1.88990.21841740.203533613535100
1.8899-1.93380.24771970.214533723569100
1.9338-1.98220.23871820.208933863568100
1.9822-2.03580.21531750.204633983573100
2.0358-2.09570.22451860.201133753561100
2.0957-2.16330.22421810.233843565100
2.1633-2.24060.22531790.198133893568100
2.2406-2.33030.23061670.192134393606100
2.3303-2.43640.20941800.181734063586100
2.4364-2.56480.1821670.188134393606100
2.5648-2.72540.20711540.190634423596100
2.7254-2.93580.21051640.183934443608100
2.9358-3.23110.21452280.185934173645100
3.2311-3.69840.19051660.178534833649100
3.6984-4.65840.16441920.155434873679100
4.6584-39.61220.20292070.1853567377498

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