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- PDB-6bh7: Phosphotriesterase variant R18+254S -

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Basic information

Entry
Database: PDB / ID: 6bh7
TitlePhosphotriesterase variant R18+254S
ComponentsPhosphotriesterase
KeywordsHYDROLASE / phosphotriesterase / organophosphate hydrolase / epistasis / directed evolution / laboratory evolution
Function / homology
Function and homology information


hydrolase activity, acting on ester bonds / catabolic process / 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-R18
Similarity search - Component
Biological speciesBrevundimonas diminuta (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsMiton, C.M. / Campbell, E.C. / Jackson, C.J. / Tokuriki, N.
CitationJournal: To Be Published
Title: Phosphotriesterase variant R18+254S
Authors: Miton, C.M. / Campbell, E.C. / Jackson, C.J. / Tokuriki, N.
History
DepositionOct 30, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 23, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Advisory / Data collection ...Advisory / 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_unobs_or_zero_occ_atoms / 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.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_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

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Assembly

Deposited unit
A: Phosphotriesterase
G: Phosphotriesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,35212
Polymers72,3632
Non-polymers98910
Water5,477304
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4890 Å2
ΔGint-206 kcal/mol
Surface area22010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.673, 86.012, 88.676
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: 36181.301 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: A0A060GYS7
#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.: 5 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6AsO2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 304 / 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: 45.52 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / Details: 100 mM NaCacodylate, 10% 2-methane-2,4-pentanediol

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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: Sep 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.35→29.042 Å / Num. obs: 142836 / % possible obs: 99.9 % / Redundancy: 14.3 % / Net I/σ(I): 14.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4CPC

4cpc


Resolution: 1.4→29.042 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1978 6399 4.95 %
Rwork0.1656 --
obs0.1672 129148 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.4→29.042 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4876 0 49 304 5229
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0126333
X-RAY DIFFRACTIONf_angle_d1.8428676
X-RAY DIFFRACTIONf_dihedral_angle_d14.5772342
X-RAY DIFFRACTIONf_chiral_restr0.121011
X-RAY DIFFRACTIONf_plane_restr0.0071135
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.41590.30542090.29354049X-RAY DIFFRACTION100
1.4159-1.43260.32621820.27134102X-RAY DIFFRACTION100
1.4326-1.450.322410.26573998X-RAY DIFFRACTION100
1.45-1.46840.29042400.24564017X-RAY DIFFRACTION100
1.4684-1.48770.29512320.24064031X-RAY DIFFRACTION100
1.4877-1.50810.26692380.22584011X-RAY DIFFRACTION100
1.5081-1.52960.24081600.21084108X-RAY DIFFRACTION100
1.5296-1.55250.26242170.20794032X-RAY DIFFRACTION100
1.5525-1.57670.26281880.20344111X-RAY DIFFRACTION100
1.5767-1.60260.26312310.18834035X-RAY DIFFRACTION100
1.6026-1.63020.24542150.18534022X-RAY DIFFRACTION100
1.6302-1.65980.23242380.17524034X-RAY DIFFRACTION100
1.6598-1.69180.21412030.1684103X-RAY DIFFRACTION100
1.6918-1.72630.20342430.16424006X-RAY DIFFRACTION100
1.7263-1.76380.22372450.16474051X-RAY DIFFRACTION100
1.7638-1.80480.20862080.16194056X-RAY DIFFRACTION100
1.8048-1.850.23512460.1614049X-RAY DIFFRACTION100
1.85-1.90.19412210.15964101X-RAY DIFFRACTION100
1.9-1.95590.2151790.16094113X-RAY DIFFRACTION100
1.9559-2.0190.21491800.16814089X-RAY DIFFRACTION100
2.019-2.09110.19861850.1624147X-RAY DIFFRACTION100
2.0911-2.17480.18442040.16044086X-RAY DIFFRACTION100
2.1748-2.27380.19681750.14824135X-RAY DIFFRACTION100
2.2738-2.39360.18122350.14794086X-RAY DIFFRACTION100
2.3936-2.54350.16461900.14694147X-RAY DIFFRACTION100
2.5435-2.73970.17741980.15844139X-RAY DIFFRACTION100
2.7397-3.01520.18212150.15824150X-RAY DIFFRACTION100
3.0152-3.45090.19891930.16424193X-RAY DIFFRACTION100
3.4509-4.34540.18171980.15134226X-RAY DIFFRACTION100
4.3454-29.04840.16592900.164322X-RAY DIFFRACTION100

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