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- PDB-4pcn: Phosphotriesterase variant R22 -

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Basic information

Entry
Database: PDB / ID: 4pcn
TitlePhosphotriesterase variant R22
ComponentsPhosphotriesterase variant PTE-R22
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
Phosphotriesterase variant PTE-R22
Similarity search - Component
Biological speciesBrevundimonas diminuta (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 Å
AuthorsJackson, C.J. / Campbell, E. / Kaltenbach, M. / Tokuriki, N.
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.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 1.4Nov 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-R22
B: Phosphotriesterase variant PTE-R22
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,29111
Polymers72,4392
Non-polymers8539
Water9,566531
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4930 Å2
ΔGint-232 kcal/mol
Surface area22360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.900, 86.266, 88.684
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
11B-515-

HOH

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Components

#1: Protein Phosphotriesterase variant PTE-R22


Mass: 36219.391 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: A0A060GSW0
#2: 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
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 531 / 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: 2.27 Å3/Da / Density % sol: 45.77 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / Details: 100 mM Na 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: Sep 11, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.54→39.44 Å / Num. obs: 97912 / % possible obs: 99.97 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.1111 / Net I/σ(I): 11.44
Reflection shellResolution: 1.54→1.595 Å / Redundancy: 7.3 % / Rmerge(I) obs: 1.237 / Mean I/σ(I) obs: 1.52 / % possible all: 100

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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: 1.54→39.437 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2051 4894 5 %
Rwork0.1703 --
obs0.172 97901 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.54→39.437 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5014 0 44 531 5589
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0155563
X-RAY DIFFRACTIONf_angle_d1.5467626
X-RAY DIFFRACTIONf_dihedral_angle_d13.6572055
X-RAY DIFFRACTIONf_chiral_restr0.079885
X-RAY DIFFRACTIONf_plane_restr0.0091003
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.54-1.55750.2821870.2443016X-RAY DIFFRACTION100
1.5575-1.57580.26361590.23723053X-RAY DIFFRACTION100
1.5758-1.5950.24941590.21773073X-RAY DIFFRACTION100
1.595-1.61520.25091530.21653094X-RAY DIFFRACTION100
1.6152-1.63650.26771640.21983043X-RAY DIFFRACTION100
1.6365-1.65890.28041610.21623088X-RAY DIFFRACTION100
1.6589-1.68260.24321620.20223055X-RAY DIFFRACTION100
1.6826-1.70770.26351770.20123061X-RAY DIFFRACTION100
1.7077-1.73440.22471560.20183089X-RAY DIFFRACTION100
1.7344-1.76280.23331740.18793073X-RAY DIFFRACTION100
1.7628-1.79320.25371550.18993108X-RAY DIFFRACTION100
1.7932-1.82580.22141540.18973045X-RAY DIFFRACTION100
1.8258-1.8610.21711630.19433077X-RAY DIFFRACTION100
1.861-1.8990.25671630.18783079X-RAY DIFFRACTION100
1.899-1.94020.2361320.18043094X-RAY DIFFRACTION100
1.9402-1.98540.20051740.17773071X-RAY DIFFRACTION100
1.9854-2.0350.21311660.17363078X-RAY DIFFRACTION100
2.035-2.090.21891550.1763123X-RAY DIFFRACTION100
2.09-2.15150.21071610.17733083X-RAY DIFFRACTION100
2.1515-2.2210.19191550.16823098X-RAY DIFFRACTION100
2.221-2.30030.20221610.16583085X-RAY DIFFRACTION100
2.3003-2.39240.22511580.16723135X-RAY DIFFRACTION100
2.3924-2.50130.19411630.16283097X-RAY DIFFRACTION100
2.5013-2.63320.19261780.16323098X-RAY DIFFRACTION100
2.6332-2.79810.18481510.16173133X-RAY DIFFRACTION100
2.7981-3.01410.20381480.16023159X-RAY DIFFRACTION100
3.0141-3.31720.18371910.15543120X-RAY DIFFRACTION100
3.3172-3.79690.17761590.14963159X-RAY DIFFRACTION100
3.7969-4.78240.16751800.13793183X-RAY DIFFRACTION100
4.7824-39.45010.20021750.1723337X-RAY DIFFRACTION100

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