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- PDB-3ood: Structure of OpdA Y257F mutant soaked with diethyl 4-methoxypheny... -

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Basic information

Entry
Database: PDB / ID: 3ood
TitleStructure of OpdA Y257F mutant soaked with diethyl 4-methoxyphenyl phosphate for 20 hours.
ComponentsPhosphotriesterase
KeywordsHYDROLASE / binuclear metallohydrolase / organophosphate hydrolysis / diethyl 4-methoxyphenyl phosphate / bioremediation / Tim Barrel / phosphotriesterase / Binuclear metal ion binding
Function / homology
Function and homology information


catabolic process / hydrolase activity, acting on ester bonds / 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 / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Prokaryotic membrane lipoprotein lipid attachment site profile. ...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 / Prokaryotic membrane lipoprotein lipid attachment site profile. / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
: / DIETHYL 4-METHOXYPHENYL PHOSPHATE / Phosphotriesterase
Similarity search - Component
Biological speciesAgrobacterium tumefaciens (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsEly, F. / Guddat, L.W. / Ollis, D.L. / Schenk, G.
CitationJournal: Biochem.J. / Year: 2010
Title: The organophosphate-degrading enzyme from Agrobacterium radiobacter displays mechanistic flexibility for catalysis.
Authors: Ely, F. / Hadler, K.S. / Gahan, L.R. / Guddat, L.W. / Ollis, D.L. / Schenk, G.
History
DepositionAug 31, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 2, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2011Group: Advisory
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Nov 1, 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_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 6, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0524
Polymers35,6741
Non-polymers3783
Water7,999444
1
A: Phosphotriesterase
hetero molecules

A: Phosphotriesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,1038
Polymers71,3472
Non-polymers7566
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area2800 Å2
ΔGint-10 kcal/mol
Surface area22630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.000, 109.000, 62.000
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Phosphotriesterase / OpdA


Mass: 35673.629 Da / Num. of mol.: 1 / Fragment: UNP residues 32-360 / Mutation: Y257F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens (bacteria) / Gene: opdA / Plasmid: pETMCSI / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q93LD7, aryldialkylphosphatase
#2: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co
#3: Chemical ChemComp-EPL / DIETHYL 4-METHOXYPHENYL PHOSPHATE


Mass: 260.223 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H17O5P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 444 / 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: 2.98 Å3/Da / Density % sol: 58.73 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 14.4 % PEG 8000, 160mM calcium acetate hydrate, 80mM sodium cacodylate, 20% glycerol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 11, 2008 / Details: Mirrors
RadiationMonochromator: Optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.89→50 Å / Num. all: 33015 / Num. obs: 33015 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.97 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 22.6
Reflection shellResolution: 1.89→50 Å / % possible all: 100

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Processing

Software
NameVersionClassification
CrystalCleardata collection
REFMAC5.2.0019refinement
CrystalCleardata reduction
CrystalCleardata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2D2J

2d2j


Resolution: 1.89→17.27 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.937 / SU B: 2.066 / SU ML: 0.064 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.19493 1676 5.1 %RANDOM
Rwork0.15478 ---
all0.15673 33015 --
obs0.15673 33015 95.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.278 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.89→17.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2509 0 19 444 2972
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222614
X-RAY DIFFRACTIONr_angle_refined_deg1.3771.9713548
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0475332
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.1322110
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.30715414
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9881527
X-RAY DIFFRACTIONr_chiral_restr0.1030.2402
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021978
X-RAY DIFFRACTIONr_nbd_refined0.2090.21486
X-RAY DIFFRACTIONr_nbtor_refined0.3070.21828
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.2384
X-RAY DIFFRACTIONr_metal_ion_refined0.0290.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1980.275
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4380.240
X-RAY DIFFRACTIONr_mcbond_it0.7111.51679
X-RAY DIFFRACTIONr_mcangle_it1.10722632
X-RAY DIFFRACTIONr_scbond_it1.97531047
X-RAY DIFFRACTIONr_scangle_it3.1624.5914
LS refinement shellResolution: 1.888→1.936 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.254 89 -
Rwork0.189 1518 -
obs--64.43 %

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