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- PDB-1ez2: THREE-DIMENSIONAL STRUCTURE OF THE ZINC-CONTAINING PHOSPHOTRIESTE... -

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Basic information

Entry
Database: PDB / ID: 1ez2
TitleTHREE-DIMENSIONAL STRUCTURE OF THE ZINC-CONTAINING PHOSPHOTRIESTERASE WITH BOUND SUBSTRATE ANALOG DIISOPROPYLMETHYL PHOSPHONATE.
ComponentsPHOSPHOTRIESTERASE
KeywordsHYDROLASE / HYDROLASE ZINC ORGANOPHOSPHATE
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
METHYLPHOSPHONIC ACID DIISOPROPYL ESTER / Parathion hydrolase
Similarity search - Component
Biological speciesBrevundimonas diminuta (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsHolden, H.M. / Benning, M.M. / Raushel, F.M. / Hong, S.-B.
CitationJournal: J.Biol.Chem. / Year: 2000
Title: The binding of substrate analogs to phosphotriesterase.
Authors: Benning, M.M. / Hong, S.B. / Raushel, F.M. / Holden, H.M.
History
DepositionMay 9, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 20, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.classification
Revision 1.4Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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_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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PHOSPHOTRIESTERASE
B: PHOSPHOTRIESTERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,5428
Polymers71,9202
Non-polymers6226
Water5,152286
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4260 Å2
ΔGint-152 kcal/mol
Surface area23030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.400, 91.000, 69.200
Angle α, β, γ (deg.)90.00, 91.60, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe biological assembly is a dimer formed by chains A and B.

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Components

#1: Protein PHOSPHOTRIESTERASE / PARATHION HYDROLASE / PTE


Mass: 35959.961 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brevundimonas diminuta (bacteria) / Plasmid: PKK01 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A434, aryldialkylphosphatase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-DII / METHYLPHOSPHONIC ACID DIISOPROPYL ESTER


Mass: 180.182 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H17O3P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 286 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.83 Å3/Da / Density % sol: 56.54 %
Crystal growTemperature: 277 K / Method: batch / pH: 9
Details: PEG 8000, Sodium Chloride, 2-Phenylethanol diisopropylmethyl phosphonate, pH 9.0, batch, temperature 277K
Crystal
*PLUS
Density % sol: 56 %
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: batch method / Details: macroseeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 mg/mlprotein11
27 %(w/v)PEG800011
3100 mM11NaCl
40.5 %(v/v)2-phenylethanol11
53 %(v/v)inhibitor11
650 mMCHES11

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: SIEMENS HI-STAR / Detector: AREA DETECTOR / Date: Oct 1, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. all: 58525 / Num. obs: 58525 / % possible obs: 92 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Rmerge(I) obs: 0.045 / Net I/σ(I): 12.3
Reflection shellResolution: 1.9→1.99 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.162 / % possible all: 78
Reflection
*PLUS
% possible obs: 88 %
Reflection shell
*PLUS
% possible obs: 78 %

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Processing

Software
NameClassification
TNTrefinement
FRAMBOdata collection
XDSdata scaling
TNTphasing
RefinementResolution: 1.9→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: TNT standard geometry
RfactorNum. reflection% reflection
all0.183 58525 -
obs0.183 58525 92 %
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5032 0 26 286 5344
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.012
X-RAY DIFFRACTIONt_angle_deg2.1
X-RAY DIFFRACTIONt_trig_c_planes0.006
X-RAY DIFFRACTIONt_gen_planes0.007
Software
*PLUS
Name: TNT / Version: 5E / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.241
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_deg2.09
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg15.8
X-RAY DIFFRACTIONt_plane_restr0.008

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