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- PDB-4xd4: Phosphotriesterase variant E2b -

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Basic information

Entry
Database: PDB / ID: 4xd4
TitlePhosphotriesterase variant E2b
ComponentsPhosphotriesterase variant PTE-R3
KeywordsHYDROLASE / dynamics / evolution / phosphotriesterase
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 / MOLECULAR REPLACEMENT / Resolution: 1.9 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
DepositionDec 19, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2015Provider: repository / Type: Initial release
Revision 1.1May 11, 2016Group: Structure summary
Revision 1.2Sep 7, 2016Group: Database references
Revision 1.3Sep 28, 2016Group: Database references
Revision 1.4Oct 26, 2016Group: Database references
Revision 1.5Sep 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 / pdbx_struct_oper_list / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _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 1.6Nov 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-R3
G: Phosphotriesterase variant PTE-R3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,14511
Polymers72,2542
Non-polymers8909
Water10,791599
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4520 Å2
ΔGint-182 kcal/mol
Surface area22380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.560, 85.782, 88.443
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-561-

HOH

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Components

#1: Protein Phosphotriesterase variant PTE-R3


Mass: 36127.230 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: A0A060GSX0
#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: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 599 / 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: 2.25 Å3/Da / Density % sol: 45.24 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / Details: 100 mM Na Cacodylate 30% 2-methane-2,4-pentanediol / PH range: 6-7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SEALED TUBE / Type: OTHER / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 22, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→39.31 Å / Num. obs: 47027 / % possible obs: 91.4 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.1183 / Net I/σ(I): 10.48
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.8233 / Mean I/σ(I) obs: 1.87 / % possible all: 92.4

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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: 1.9→39.306 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2434 2618 5.57 %
Rwork0.175 --
obs0.1787 46964 90.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→39.306 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5020 0 38 599 5657
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075303
X-RAY DIFFRACTIONf_angle_d1.0627224
X-RAY DIFFRACTIONf_dihedral_angle_d13.3071938
X-RAY DIFFRACTIONf_chiral_restr0.04836
X-RAY DIFFRACTIONf_plane_restr0.005941
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.93450.37541330.28892328X-RAY DIFFRACTION92
1.9345-1.97180.33621310.27832348X-RAY DIFFRACTION92
1.9718-2.0120.321680.24952295X-RAY DIFFRACTION92
2.012-2.05570.28611260.23062361X-RAY DIFFRACTION92
2.0557-2.10360.3072990.21222363X-RAY DIFFRACTION91
2.1036-2.15620.27041370.20922324X-RAY DIFFRACTION91
2.1562-2.21450.28281150.22326X-RAY DIFFRACTION91
2.2145-2.27960.25191510.19872310X-RAY DIFFRACTION90
2.2796-2.35320.2491360.19542317X-RAY DIFFRACTION91
2.3532-2.43730.23371790.18092276X-RAY DIFFRACTION90
2.4373-2.53490.25141460.18092330X-RAY DIFFRACTION91
2.5349-2.65020.26511140.1832341X-RAY DIFFRACTION91
2.6502-2.78990.24431450.16852330X-RAY DIFFRACTION90
2.7899-2.96460.25691660.17592326X-RAY DIFFRACTION91
2.9646-3.19340.23261840.16262318X-RAY DIFFRACTION91
3.1934-3.51460.24931250.16092373X-RAY DIFFRACTION91
3.5146-4.02270.20521530.14012345X-RAY DIFFRACTION90
4.0227-5.06650.17111020.12552395X-RAY DIFFRACTION89
5.0665-39.31440.19681080.15212340X-RAY DIFFRACTION83

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