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- PDB-1i0d: HIGH RESOLUTION STRUCTURE OF THE ZINC/CADMIUM-CONTAINING PHOSPHOT... -

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Basic information

Entry
Database: PDB / ID: 1i0d
TitleHIGH RESOLUTION STRUCTURE OF THE ZINC/CADMIUM-CONTAINING PHOSPHOTRIESTERASE FROM PSEUDOMONAS DIMINUTA
ComponentsPHOSPHOTRIESTERASE
KeywordsHYDROLASE / PTE / Zinc / Cadmium / mixed metals
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
: / FORMIC ACID / 2-PHENYL-ETHANOL / Parathion hydrolase
Similarity search - Component
Biological speciesBrevundimonas diminuta (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.3 Å
AuthorsHolden, H.M. / Benning, M.M. / Raushel, F.M. / Shim, H.
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
DepositionJan 29, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PHOSPHOTRIESTERASE
B: PHOSPHOTRIESTERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,61727
Polymers71,9482
Non-polymers1,66925
Water13,277737
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5770 Å2
ΔGint-101 kcal/mol
Surface area23940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.444, 90.034, 68.385
Angle α, β, γ (deg.)90.00, 91.72, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe biological assembly is a dimer

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein PHOSPHOTRIESTERASE / PARATHION HYDROLASE / PTE


Mass: 35974.008 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: P0A434, aryldialkylphosphatase

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Non-polymers , 7 types, 762 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cd
#4: Chemical ChemComp-NA / SODIUM ION


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


Mass: 62.068 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-PEL / 2-PHENYL-ETHANOL


Mass: 122.164 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10O
#7: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 737 / 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: 2.75 Å3/Da / Density % sol: 55.2 %
Crystal growTemperature: 277 K / Method: batch / pH: 9
Details: peg 8000, sodium chloride, phenethyl alcohol, CHES, pH 9.0, batch, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / 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: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.71 Å
DetectorType: SBC-1 / Detector: CCD / Date: Jul 7, 2000
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: 190056 / Num. obs: 190056 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 30.3
Reflection shellResolution: 1.3→1.37 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.31 / % possible all: 99
Reflection
*PLUS
Num. measured all: 1626798
Reflection shell
*PLUS
% possible obs: 99 % / Mean I/σ(I) obs: 2.8

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Processing

Software
NameClassification
TNTrefinement
DENZOdata reduction
SCALEPACKdata scaling
TNTphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.3→30 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: tnt standard geometry
RfactorNum. reflectionSelection details
Rfree0.224 9355 random
Rwork0.191 --
all0.193 190056 -
obs0.193 190056 -
Refinement stepCycle: LAST / Resolution: 1.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5094 0 92 737 5923
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.011
X-RAY DIFFRACTIONt_angle_deg2.2
X-RAY DIFFRACTIONt_dihedral_angle_d14.65
X-RAY DIFFRACTIONt_trig_c_planes0.007
X-RAY DIFFRACTIONt_gen_planes0.009
Software
*PLUS
Name: TNT / Version: 5E / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg14.65
X-RAY DIFFRACTIONt_plane_restr0.009

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