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- PDB-4pbe: Phosphotriesterase Variant Rev6 -

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Basic information

Entry
Database: PDB / ID: 4pbe
TitlePhosphotriesterase Variant Rev6
ComponentsPhosphotriesterase variant PTE-revR6
KeywordsHYDROLASE / Phosphotriesterase / Arylesterase / 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-revR6
Similarity search - Component
Biological speciesBrevundimonas diminuta (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.51 Å
AuthorsCampbell, E. / Kaltenbach, M. / Tokuriki, N. / Jackson, C.J.
CitationJournal: Nat. Chem. Biol. / Year: 2016
Title: The role of protein dynamics in the evolution of new enzyme function.
Authors: Campbell, E. / Kaltenbach, M. / Correy, G.J. / Carr, P.D. / Porebski, B.T. / Livingstone, E.K. / Afriat-Jurnou, L. / Buckle, A.M. / Weik, M. / Hollfelder, F. / Tokuriki, N. / Jackson, C.J.
History
DepositionApr 12, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 7, 2016Group: Database references
Revision 1.2Apr 18, 2018Group: Data collection / Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / diffrn_source / pdbx_struct_oper_list
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Sep 27, 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 1.4Nov 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 variant PTE-revR6
G: Phosphotriesterase variant PTE-revR6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,1128
Polymers72,5952
Non-polymers5176
Water9,584532
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4170 Å2
ΔGint-176 kcal/mol
Surface area22860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.638, 85.966, 89.188
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 variant PTE-revR6


Mass: 36297.523 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brevundimonas diminuta (bacteria) / Gene: opd / Production host: Escherichia coli (E. coli) / References: UniProt: A0A060GPP4, aryldialkylphosphatase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6AsO2
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 532 / 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: 45.6 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / Details: 100 mM Cacodylate, 35% 2-methyl-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: Jan 21, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.5→39.58 Å / Num. obs: 105280 / % possible obs: 99.9 % / Redundancy: 7.3 % / Net I/σ(I): 16.1

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
MOLREPphasing
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GY0

4gy0


Resolution: 1.51→39.585 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2488 5162 4.98 %RANDOM
Rwork0.2096 ---
obs0.2115 103647 99.95 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.51→39.585 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5070 0 17 532 5619
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075277
X-RAY DIFFRACTIONf_angle_d1.1157174
X-RAY DIFFRACTIONf_dihedral_angle_d13.1191931
X-RAY DIFFRACTIONf_chiral_restr0.044832
X-RAY DIFFRACTIONf_plane_restr0.005932
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.51-1.52720.34541630.3213192X-RAY DIFFRACTION99
1.5272-1.54520.3571980.31123221X-RAY DIFFRACTION100
1.5452-1.5640.30251500.31343274X-RAY DIFFRACTION100
1.564-1.58380.3371820.2943240X-RAY DIFFRACTION100
1.5838-1.60460.35941740.29223229X-RAY DIFFRACTION100
1.6046-1.62660.28571560.28883277X-RAY DIFFRACTION100
1.6266-1.64990.29921730.29023255X-RAY DIFFRACTION100
1.6499-1.67450.32431780.27893233X-RAY DIFFRACTION100
1.6745-1.70070.28821610.26613242X-RAY DIFFRACTION100
1.7007-1.72850.33421700.27363272X-RAY DIFFRACTION100
1.7285-1.75830.29441630.2683272X-RAY DIFFRACTION100
1.7583-1.79030.35011610.26543276X-RAY DIFFRACTION100
1.7903-1.82480.30991660.26523264X-RAY DIFFRACTION100
1.8248-1.8620.28651680.25683270X-RAY DIFFRACTION100
1.862-1.90250.27941450.25323304X-RAY DIFFRACTION100
1.9025-1.94670.31071800.25243215X-RAY DIFFRACTION100
1.9467-1.99540.2871450.24843333X-RAY DIFFRACTION100
1.9954-2.04940.28791760.2333235X-RAY DIFFRACTION100
2.0494-2.10970.27031810.22853256X-RAY DIFFRACTION100
2.1097-2.17780.2691890.21873302X-RAY DIFFRACTION100
2.1778-2.25560.23511910.20473256X-RAY DIFFRACTION100
2.2556-2.34590.23741700.21073269X-RAY DIFFRACTION100
2.3459-2.45260.24081580.19783310X-RAY DIFFRACTION100
2.4526-2.58190.2251760.19763310X-RAY DIFFRACTION100
2.5819-2.74370.23241760.19533299X-RAY DIFFRACTION100
2.7437-2.95540.21351660.18623337X-RAY DIFFRACTION100
2.9554-3.25270.22181880.17813297X-RAY DIFFRACTION100
3.2527-3.72310.22271730.16543361X-RAY DIFFRACTION100
3.7231-4.68950.17451920.15063371X-RAY DIFFRACTION100
4.6895-39.59850.23191930.17273513X-RAY DIFFRACTION100

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