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- PDB-4e3t: Round 18 Arylesterase Variant of Phosphotriesterase with Bound Tr... -

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Basic information

Entry
Database: PDB / ID: 4e3t
TitleRound 18 Arylesterase Variant of Phosphotriesterase with Bound Transition State Analog
ComponentsPhosphotriesterase
KeywordsHYDROLASE / phosphotriesterase / 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
hexyl(naphthalen-2-yloxy)phosphinic acid / Parathion hydrolase
Similarity search - Component
Biological speciesBrevundimonas diminuta (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsTokuriki, N. / Jackson, C.J. / 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
DepositionMar 10, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 23, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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 / pdbx_initial_refinement_model / 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

Downloads & links

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Assembly

Deposited unit
A: Phosphotriesterase
B: Phosphotriesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,1029
Polymers72,4172
Non-polymers6857
Water8,107450
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2850 Å2
ΔGint-8 kcal/mol
Surface area22540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.771, 85.975, 88.727
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


Mass: 36208.414 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: 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-HLN / hexyl(naphthalen-2-yloxy)phosphinic acid


Mass: 292.310 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H21O3P
#4: 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 HAS BEEN DEPOSITED TO GENBANK, AFL46607.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.54 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 50mM MES, 2% PEG8000, 30% MPD, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 20, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9393 Å / Relative weight: 1
ReflectionResolution: 1.65→30 Å / Num. obs: 79417 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 18.42 Å2
Reflection shellResolution: 1.65→1.74 Å / % possible all: 99.5

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Processing

Software
NameVersionClassification
DNAdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2R1N

2r1n


Resolution: 1.65→29.576 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.865 / SU ML: 0.42 / σ(F): 1.33 / Phase error: 20.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2055 3988 5.03 %5
Rwork0.1733 ---
obs0.1749 75264 99.78 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.814 Å2 / ksol: 0.347 e/Å3
Displacement parametersBiso max: 110.83 Å2 / Biso mean: 26.5965 Å2 / Biso min: 6.87 Å2
Baniso -1Baniso -2Baniso -3
1--1.669 Å20 Å2-0 Å2
2--6.7365 Å20 Å2
3----5.0675 Å2
Refinement stepCycle: LAST / Resolution: 1.65→29.576 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5000 0 26 450 5476
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0215573
X-RAY DIFFRACTIONf_angle_d1.8947625
X-RAY DIFFRACTIONf_chiral_restr0.148893
X-RAY DIFFRACTIONf_plane_restr0.013995
X-RAY DIFFRACTIONf_dihedral_angle_d14.1032077
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 28

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.65-1.67010.32761300.28242633276398
1.6701-1.69130.26791240.26482673279799
1.6913-1.71350.28041490.249526512800100
1.7135-1.7370.30031610.242826162777100
1.737-1.76180.27691430.228327032846100
1.7618-1.78810.23831420.218926442786100
1.7881-1.8160.23861490.211126562805100
1.816-1.84580.25511380.206326502788100
1.8458-1.87760.24851230.187126952818100
1.8776-1.91180.22311410.186226632804100
1.9118-1.94850.22431360.178226742810100
1.9485-1.98830.21481450.195126842829100
1.9883-2.03150.24141530.180126652818100
2.0315-2.07880.20781510.180326412792100
2.0788-2.13070.22311450.180627022847100
2.1307-2.18830.20221410.180426592800100
2.1883-2.25270.22411480.168126992847100
2.2527-2.32540.20721430.17126742817100
2.3254-2.40840.21061500.167426682818100
2.4084-2.50480.18231490.164626952844100
2.5048-2.61880.20721490.162127022851100
2.6188-2.75670.18361240.153727232847100
2.7567-2.92930.171380.155227002838100
2.9293-3.15520.20271520.162327192871100
3.1552-3.47230.22141550.160727052860100
3.4723-3.97380.15271410.149127452886100
3.9738-5.00260.16961360.13572781291799
5.0026-29.58040.20911320.20152912304499
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.6764-0.0286-0.09291.6739-0.02560.8658-0.00140.08330.0397-0.05060.00220.02980.0142-0.0195-0.01120.0971-0.01730.00160.03810.01310.114118.516923.45315.7444
22.4698-0.32910.10061.45830.42352.06570.0353-0.4547-0.54280.55820.0170.67390.5037-0.5859-0.0530.2826-0.07860.06890.27920.08110.27344.968114.697-0.795
31.59440.1437-0.23641.5483-0.39891.82350.03550.3387-0.1253-0.2243-0.0880.05690.1161-0.1570.02630.18150.0144-0.00560.1041-0.03990.132714.7514.5625-6.4956
40.4676-0.18870.42610.14080.08371.4956-0.0208-0.55780.0070.06420.0286-0.0841-0.07860.19460.03450.1091-0.0185-0.01010.4247-0.03580.138925.165226.749138.3749
50.78830.16440.34390.36860.01610.6878-0.0826-0.5441-0.05480.05010.04280.04890.02070.05290.01240.06530.00650.02750.31040.05520.088412.274917.266635.3714
60.3920.0782-0.31880.0332-0.02690.60450.0599-0.62860.15320.1540.06020.0407-0.20820.0655-0.12920.01680.01370.2020.6166-0.1631-0.065910.034631.510447.678
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 36:244)A36 - 244
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 245:276)A245 - 276
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 277:362)A277 - 362
4X-RAY DIFFRACTION4CHAIN B AND (RESSEQ 36:92)B36 - 92
5X-RAY DIFFRACTION5CHAIN B AND (RESSEQ 93:219)B93 - 219
6X-RAY DIFFRACTION6CHAIN B AND (RESSEQ 220:361)B220 - 361

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