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- PDB-6b2f: Phosphotriesterase variant S5 + TS analogue -

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Basic information

Entry
Database: PDB / ID: 6b2f
TitlePhosphotriesterase variant S5 + TS analogue
ComponentsPhosphotriesterase
KeywordsHYDROLASE / phosphotriesterase / organophosphate hydrolase / epistasis / directed evolution / laboratory evolution
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
hexyl(naphthalen-2-yloxy)phosphinic acid / Phosphotriesterase variant PTE-R0
Similarity search - Component
Biological speciesBrevundimonas diminuta (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.775 Å
AuthorsMiton, C.M. / Campbell, E.C. / Jackson, C.J. / Tokuriki, N.
CitationJournal: To Be Published
Title: Phosphotriesterase variant S5 + TS analogue
Authors: Miton, C.M. / Campbell, E.C. / Jackson, C.J. / Tokuriki, N.
History
DepositionSep 20, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 23, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 4, 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 / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 1.2Nov 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
G: Phosphotriesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,24714
Polymers71,6922
Non-polymers1,55512
Water4,954275
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4120 Å2
ΔGint-51 kcal/mol
Surface area22980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.660, 85.020, 87.940
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: 35845.840 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brevundimonas diminuta (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A060GYS1
#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.: 6 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-HLN / hexyl(naphthalen-2-yloxy)phosphinic acid


Mass: 292.310 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H21O3P / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 275 / 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: 2.38 Å3/Da / Density % sol: 48.38 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop
Details: 100 mM MES, 10% 2-methane-2,4-pentanediol, 4 molar equivalent HLN

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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: Mar 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.77→30.562 Å / Num. obs: 60736 / % possible obs: 98.2 % / Redundancy: 5.6 % / Net I/σ(I): 6.9

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4CPC

4cpc


Resolution: 1.775→30.562 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.9
RfactorNum. reflection% reflection
Rfree0.2295 3055 5.04 %
Rwork0.1957 --
obs0.1974 60648 97.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.775→30.562 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4882 0 92 275 5249
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0145269
X-RAY DIFFRACTIONf_angle_d0.987147
X-RAY DIFFRACTIONf_dihedral_angle_d15.8183151
X-RAY DIFFRACTIONf_chiral_restr0.055824
X-RAY DIFFRACTIONf_plane_restr0.006919
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.775-1.80270.38661230.36912544X-RAY DIFFRACTION96
1.8027-1.83230.41761350.3542555X-RAY DIFFRACTION97
1.8323-1.86390.32391330.3292567X-RAY DIFFRACTION97
1.8639-1.89780.361350.31672591X-RAY DIFFRACTION97
1.8978-1.93430.33991360.30512599X-RAY DIFFRACTION97
1.9343-1.97370.29081350.28242569X-RAY DIFFRACTION97
1.9737-2.01660.26921420.26422533X-RAY DIFFRACTION97
2.0166-2.06350.28671150.25482590X-RAY DIFFRACTION97
2.0635-2.11510.25641270.2322573X-RAY DIFFRACTION97
2.1151-2.17230.25771360.21652546X-RAY DIFFRACTION96
2.1723-2.23620.24331320.2072550X-RAY DIFFRACTION96
2.2362-2.30840.26431420.2032589X-RAY DIFFRACTION96
2.3084-2.39080.24131400.18922552X-RAY DIFFRACTION97
2.3908-2.48650.22281320.18792588X-RAY DIFFRACTION97
2.4865-2.59960.26191470.18692611X-RAY DIFFRACTION98
2.5996-2.73660.24341380.18482639X-RAY DIFFRACTION99
2.7366-2.90790.21411470.17172687X-RAY DIFFRACTION100
2.9079-3.13230.21231410.16282691X-RAY DIFFRACTION100
3.1323-3.44710.19551510.15752687X-RAY DIFFRACTION100
3.4471-3.9450.19451510.14752711X-RAY DIFFRACTION100
3.945-4.96680.15661760.14582731X-RAY DIFFRACTION100
4.9668-30.56670.20121410.17882890X-RAY DIFFRACTION100
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)
10.33380.0223-0.02640.48970.28810.5161-0.00360.04440.0474-0.05330.037-0.1023-0.12460.06070.02070.0668-0.00360.0170.17980.01220.192729.55324.52577.2922
20.87050.2392-0.2250.3360.02630.7970.0220.0382-0.0142-0.0083-0.028-0.02460.0068-0.0747-00.08560.0173-0.00940.138-0.00550.155915.217216.84786.8977
30.24190.2313-0.14710.27770.06450.1707-0.09830.1498-0.1232-0.24740.1617-0.05180.1852-0.11540.00220.2758-0.00450.0030.2593-0.05420.198922.94038.2887-10.3409
40.1756-0.0075-0.17550.67450.41870.4277-0.06220.0847-0.0397-0.13790.1397-0.0963-0.09010.17680.00030.118-0.00060.0380.2189-0.01860.181329.841516.1522-4.733
50.0455-0.0112-0.02720.0022-0.02440.0406-0.0640.046-0.01490.4773-0.0401-0.12010.0237-0.010600.3614-0.0092-0.09780.15830.00120.211129.122725.071948.0914
60.21470.161-0.1020.1369-0.01620.1274-0.06650.01840.02530.33560.00570.062-0.1809-0.083900.22730.02010.0270.1663-0.01010.163611.981824.4434.4683
70.2949-0.0012-0.01840.3944-0.16681.09920.02960.032-0.00210.1416-0.0472-0.0430.11320.053-00.22380.0154-0.0340.1433-0.00210.160225.635911.668435.3632
80.11860.085-0.21150.3035-0.10040.1786-0.119-0.15690.01270.45310.11350.06450.0569-0.1033-0.00040.37750.0104-0.00320.15780.0010.170717.83242.97747.6759
90.1561-0.1336-0.13670.11470.04670.1121-0.0843-0.1533-0.15750.42440.01550.17450.3095-0.0344-0.01560.429-0.08020.06120.21960.00220.24527.41593.688250.9643
100.1541-0.0023-0.06430.3782-0.19970.3343-0.03180.0009-0.02580.32070.06960.0601-0.0112-0.0603-00.36770.00650.04710.19840.00180.182811.791215.384448.872
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 34 through 92 )
2X-RAY DIFFRACTION2chain 'A' and (resid 93 through 236 )
3X-RAY DIFFRACTION3chain 'A' and (resid 237 through 298 )
4X-RAY DIFFRACTION4chain 'A' and (resid 299 through 364 )
5X-RAY DIFFRACTION5chain 'G' and (resid 33 through 49 )
6X-RAY DIFFRACTION6chain 'G' and (resid 50 through 92 )
7X-RAY DIFFRACTION7chain 'G' and (resid 93 through 219 )
8X-RAY DIFFRACTION8chain 'G' and (resid 220 through 259 )
9X-RAY DIFFRACTION9chain 'G' and (resid 260 through 298 )
10X-RAY DIFFRACTION10chain 'G' and (resid 299 through 364 )

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