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- PDB-4pcp: Crystal structure of Phosphotriesterase variant R0 -

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Basic information

Entry
Database: PDB / ID: 4pcp
TitleCrystal structure of Phosphotriesterase variant R0
ComponentsPhosphotriesterase variant PTE-R0
KeywordsHYDROLASE / Phosphotriesterase / arylesterase / evolution
Function / homology
Function and homology information


aryldialkylphosphatase / 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 / Parathion hydrolase
Similarity search - Component
Biological speciesBrevundimonas diminuta (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 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 16, 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

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Assembly

Deposited unit
A: Phosphotriesterase variant PTE-R0
G: Phosphotriesterase variant PTE-R0
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,6488
Polymers72,1122
Non-polymers5366
Water6,900383
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3880 Å2
ΔGint-156 kcal/mol
Surface area22970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.141, 86.325, 88.722
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11G-2542-

HOH

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Components

#1: Protein Phosphotriesterase variant PTE-R0


Mass: 36056.129 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: A0A060GYS1, 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.: 2 / Source method: obtained synthetically / Formula: C2H6AsO2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 383 / 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: 2.29 Å3/Da / Density % sol: 46.22 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / Details: 100 mM cacodylate, 30% 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: Apr 18, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.63→43.2 Å / Num. obs: 83078 / % possible obs: 99.98 % / Redundancy: 7.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.101 / Net I/σ(I): 13.19
Reflection shellResolution: 1.63→1.68 Å / Redundancy: 7.4 % / Mean I/σ(I) obs: 2.35 / Num. measured obs: 8191 / CC1/2: 0.83 / % possible all: 99.99

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Processing

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

4gy0


Resolution: 1.63→43.163 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.219 4159 5.01 %
Rwork0.1789 --
obs0.1809 83054 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.63→43.163 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5028 0 14 383 5425
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095538
X-RAY DIFFRACTIONf_angle_d1.1817580
X-RAY DIFFRACTIONf_dihedral_angle_d13.2372051
X-RAY DIFFRACTIONf_chiral_restr0.049877
X-RAY DIFFRACTIONf_plane_restr0.0061001
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.63-1.64850.3161190.2642603X-RAY DIFFRACTION100
1.6485-1.66790.32021270.25312607X-RAY DIFFRACTION100
1.6679-1.68830.26841300.23972605X-RAY DIFFRACTION100
1.6883-1.70960.26581400.23262577X-RAY DIFFRACTION100
1.7096-1.73210.29151440.22882597X-RAY DIFFRACTION100
1.7321-1.75590.28271540.22332595X-RAY DIFFRACTION100
1.7559-1.78090.28321190.22012606X-RAY DIFFRACTION100
1.7809-1.80750.2621230.21832637X-RAY DIFFRACTION100
1.8075-1.83580.28531350.21462612X-RAY DIFFRACTION100
1.8358-1.86590.29551560.20442573X-RAY DIFFRACTION100
1.8659-1.8980.24611330.20622606X-RAY DIFFRACTION100
1.898-1.93260.2361350.20152632X-RAY DIFFRACTION100
1.9326-1.96970.2471490.20992602X-RAY DIFFRACTION100
1.9697-2.00990.26041430.20212604X-RAY DIFFRACTION100
2.0099-2.05360.23981230.19382607X-RAY DIFFRACTION100
2.0536-2.10140.23011280.19532654X-RAY DIFFRACTION100
2.1014-2.1540.25711400.19012595X-RAY DIFFRACTION100
2.154-2.21220.21561360.19012640X-RAY DIFFRACTION100
2.2122-2.27730.21881470.19012600X-RAY DIFFRACTION100
2.2773-2.35080.24221350.18112614X-RAY DIFFRACTION100
2.3508-2.43480.20251490.17842631X-RAY DIFFRACTION100
2.4348-2.53230.19971370.1792634X-RAY DIFFRACTION100
2.5323-2.64750.21331330.17962639X-RAY DIFFRACTION100
2.6475-2.78710.22611460.17512656X-RAY DIFFRACTION100
2.7871-2.96160.20191600.17022617X-RAY DIFFRACTION100
2.9616-3.19030.23371490.16892643X-RAY DIFFRACTION100
3.1903-3.51120.20761530.16282642X-RAY DIFFRACTION100
3.5112-4.01890.17251400.14682695X-RAY DIFFRACTION100
4.0189-5.06220.18091230.1382746X-RAY DIFFRACTION100
5.0622-43.17760.17711530.16662826X-RAY DIFFRACTION99

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