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- PDB-1jgm: High Resolution Structure of the Cadmium-containing Phosphotriest... -

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Basic information

Entry
Database: PDB / ID: 1jgm
TitleHigh Resolution Structure of the Cadmium-containing Phosphotriesterase from Pseudomonas diminuta
ComponentsPhosphotriesterase
KeywordsHYDROLASE / PTE / Cadmium
Function / homology
Function and homology information


aryldialkylphosphatase activity / aryldialkylphosphatase / 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
: / 2-PHENYL-ETHANOL / Parathion hydrolase
Similarity search - Component
Biological speciesBrevundimonas diminuta (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.3 Å
AuthorsBenning, M.M. / Shim, H. / Raushel, F.M. / Holden, H.M.
CitationJournal: Biochemistry / Year: 2001
Title: High resolution X-ray structures of different metal-substituted forms of phosphotriesterase from Pseudomonas diminuta.
Authors: Benning, M.M. / Shim, H. / Raushel, F.M. / Holden, H.M.
History
DepositionJun 26, 2001Deposition site: RCSB / Processing site: RCSB
SupersessionJul 4, 2001ID: 1I03
Revision 1.0Jul 4, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 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_conn_type / 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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.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 / _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)75,28938
Polymers72,7512
Non-polymers2,53836
Water13,331740
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8000 Å2
ΔGint-10 kcal/mol
Surface area23760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.450, 90.030, 68.390
Angle α, β, γ (deg.)90.00, 91.72, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe biological asembly is a dimer that is described by chains A & B in the asymmetric unit

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Phosphotriesterase / PARATHION HYDROLASE / PTE


Mass: 36375.402 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brevundimonas diminuta (bacteria) / Gene: OPD / Production host: Escherichia coli (E. coli) / References: UniProt: P0A434, aryldialkylphosphatase

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Non-polymers , 5 types, 776 molecules

#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cd
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 27 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PEL / 2-PHENYL-ETHANOL


Mass: 122.164 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H10O
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 740 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.72 Å3/Da / Density % sol: 54.7 %
Crystal growTemperature: 277 K / Method: batch/microseeding / pH: 9
Details: PEG-8000, sodium chloride, phenylethyl alcohol, diethyl-4-methylbenzylphosphate, CHES, pH 9, Batch/microseeding, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 9 / Method: vapor diffusion, hanging drop / Details: Benning, M.M., (1995) Biochemistry, 34, 7973.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
111 mg/mlprotein1drop
210 %PEG80001reservoir
35 mM1reservoirNaN3
41 %(v/v)2-phenylethanol1reservoir
550 mMCHES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.71 Å
DetectorType: SBC-2 / Detector: CCD / Date: Dec 17, 1999
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.71 Å / Relative weight: 1
ReflectionResolution: 1.3→30 Å / Num. all: 187426 / Num. obs: 187426 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 32
Reflection shellResolution: 1.3→1.37 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.184 / % possible all: 99
Reflection
*PLUS
Num. measured all: 1231444
Reflection shell
*PLUS
% possible obs: 99 %

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Processing

Software
NameClassification
TNTrefinement
d*TREKdata reduction
HKL-2000data scaling
TNTphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.3→30 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.236 9243 4.9 %random
Rwork0.202 ---
all0.204 187426 --
obs0.204 187426 --
Refinement stepCycle: LAST / Resolution: 1.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5110 0 147 740 5997
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_deg2.1
X-RAY DIFFRACTIONt_bond_d0.011
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 4.9 % / Rfactor all: 0.204 / Rfactor Rwork: 0.202
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: t_angle_deg / Dev ideal: 2.1

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