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- PDB-4zsu: Crystal structure of Brevundimonas diminuta phosphotriesterase mu... -

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Basic information

Entry
Database: PDB / ID: 4zsu
TitleCrystal structure of Brevundimonas diminuta phosphotriesterase mutant L7eP-3aG
ComponentsParathion hydrolase
KeywordsHYDROLASE / Bacterial Proteins / Enzymes / Catalysis / Amidohydrolase / Chemical Warfare Agents / VX nerve agent / VR nerve agent
Function / homology
Function and homology information


aryldialkylphosphatase / aryldialkylphosphatase activity / catabolic process / zinc ion binding / plasma membrane
Similarity search - Function
Aryldialkylphosphatase, zinc-binding site / Phosphotriesterase family signature 1. / Phosphotriesterase / Phosphotriesterase family / Phosphotriesterase family profile. / Metal-dependent hydrolases / Metal-dependent hydrolase / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / TIM Barrel ...Aryldialkylphosphatase, zinc-binding site / Phosphotriesterase family signature 1. / Phosphotriesterase / Phosphotriesterase family / Phosphotriesterase family profile. / Metal-dependent hydrolases / Metal-dependent hydrolase / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
: / Parathion hydrolase
Similarity search - Component
Biological speciesBrevundimonas diminuta (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.011 Å
AuthorsMabanglo, M.F. / Raushel, F.M.
CitationJournal: Biochemistry / Year: 2015
Title: Variants of Phosphotriesterase for the Enhanced Detoxification of the Chemical Warfare Agent VR.
Authors: Bigley, A.N. / Mabanglo, M.F. / Harvey, S.P. / Raushel, F.M.
History
DepositionMay 14, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 23, 2015Group: Database references
Revision 1.2Jun 1, 2016Group: Data collection
Revision 1.3Nov 20, 2019Group: Derived calculations
Category: pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn
Item: _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Sep 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 1.5Nov 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: Parathion hydrolase
B: Parathion hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,3096
Polymers73,0732
Non-polymers2364
Water6,521362
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3230 Å2
ΔGint-62 kcal/mol
Surface area22820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.485, 80.634, 78.839
Angle α, β, γ (deg.)90.000, 106.940, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Parathion hydrolase / Phosphotriesterase / PTE


Mass: 36536.664 Da / Num. of mol.: 2 / Fragment: residues 36-363
Mutation: I106C, F132V, H254Q, H257Y, A270V, L272M, I274N, S308L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brevundimonas diminuta (bacteria) / Gene: opd / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0A434, aryldialkylphosphatase
#2: Chemical
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Co
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 362 / 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: 1.93 Å3/Da / Density % sol: 36.43 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 100 mM sodium cacodylate pH 5.5-7.0, 0.2 M magnesium acetate, 15-30% PEG 8000
PH range: 5.5-7.0

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Nov 7, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
Reflection twinOperator: h,-k,-h-l / Fraction: 0.31
ReflectionResolution: 2→50 Å / Num. obs: 34657 / % possible obs: 95.8 % / Redundancy: 3.7 % / Net I/σ(I): 18.9

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: dev_1108)refinement
SCALEPACKdata scaling
PDB_EXTRACT3.15data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DPM

1dpm


Resolution: 2.011→29.573 Å / FOM work R set: 0.8459 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.18 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.1838 2081 6 %
Rwork0.1348 32640 -
obs0.1395 34657 95.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 94.33 Å2 / Biso mean: 28.08 Å2 / Biso min: 18.13 Å2
Refinement stepCycle: final / Resolution: 2.011→29.573 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5029 0 4 362 5395
Biso mean--30.6 38.4 -
Num. residues----658
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075117
X-RAY DIFFRACTIONf_angle_d1.1026948
X-RAY DIFFRACTIONf_chiral_restr0.067812
X-RAY DIFFRACTIONf_plane_restr0.005899
X-RAY DIFFRACTIONf_dihedral_angle_d14.5541863
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0111-2.06140.25741400.2222180232084
2.0614-2.11710.29491310.20232229236089
2.1171-2.17940.23611420.18442269241188
2.1794-2.24970.21461440.17822324246889
2.2497-2.330.24491370.17032288242590
2.33-2.42330.22181450.16112324246989
2.4233-2.53350.21331440.15342326247090
2.5335-2.66690.18821410.15382328246991
2.6669-2.83380.20731430.14252375251891
2.8338-3.05220.18281490.13462355250491
3.0522-3.35880.15881490.13072353250291
3.3588-3.84330.17541450.11382402254792
3.8433-4.83670.12871510.09582414256592
4.8367-25.32020.14781450.11552473261893
Refinement TLS params.Method: refined / Origin x: 48.1751 Å / Origin y: 1.1662 Å / Origin z: 20.8945 Å
111213212223313233
T0.3066 Å2-0.001 Å2-0.0654 Å2-0.156 Å20.0023 Å2--0.2248 Å2
L0.1314 °2-0.014 °2-0.0588 °2-0.118 °20.0987 °2--0.5499 °2
S-0.0096 Å °0.0023 Å °0.0009 Å °-0.0024 Å °-0.0036 Å °0.0031 Å °0.0035 Å °0.0033 Å °0.0141 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA35 - 363
2X-RAY DIFFRACTION1allB35 - 363
3X-RAY DIFFRACTION1allC1
4X-RAY DIFFRACTION1allD1
5X-RAY DIFFRACTION1allE1
6X-RAY DIFFRACTION1allF1
7X-RAY DIFFRACTION1allS1 - 384

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