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- PDB-2zc1: Organophosphorus Hydrolase from Deinococcus radiodurans -

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Basic information

Entry
Database: PDB / ID: 2zc1
TitleOrganophosphorus Hydrolase from Deinococcus radiodurans
ComponentsPhosphotriesterase
KeywordsHYDROLASE / alpha beta barrel / bi-nuclear metal active-site / carboxylated lysine
Function / homology
Function and homology information


lactonohydrolase activity / catabolic process / 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 / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
BROMIDE ION / : / Phosphotriesterase, putative
Similarity search - Component
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsLarsen, S.D. / Hawwa, R. / Ratia, K. / Santarsiero, B.D. / Mesecar, A.D.
CitationJournal: to be published
Title: X-Ray Structural Insights into a Phosphotriesterase
Authors: Larsen, S.D. / Hawwa, R. / Ratia, K. / Santarsiero, B.D. / Mesecar, A.D.
History
DepositionNov 2, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 25, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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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)36,2277
Polymers35,7891
Non-polymers4376
Water8,485471
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Phosphotriesterase
hetero molecules

A: Phosphotriesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,45314
Polymers71,5782
Non-polymers87512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area4630 Å2
ΔGint-75 kcal/mol
Surface area23320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.843, 60.843, 207.694
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-528-

HOH

21A-544-

HOH

31A-565-

HOH

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Components

#1: Protein Phosphotriesterase / Organophosphorus Hydrolase


Mass: 35789.195 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans (radioresistant)
Strain: R1 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9RVU2, aryldialkylphosphatase
#2: Chemical
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Br
#3: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 471 / 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: 3.1 Å3/Da / Density % sol: 60.35 %
Crystal growTemperature: 296 K / pH: 4.6
Details: 20mM Calcium Chloride, 100mM Sodium Acetate, 31% 2-methyl-2,4-pentanediol, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-D / Wavelength: 0.9198,0.9195, 0.9093
DetectorType: ADSC Q4 CCD / Detector: CCD / Date: Dec 27, 2001 / Details: MIRRORS
RadiationMonochromator: MIRRORS / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.91981
20.91951
30.90931
ReflectionResolution: 1.9→20 Å / Num. obs: 270178 / % possible obs: 99.2 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.061 / Net I/σ(I): 23.6
Reflection shellResolution: 1.9→2 Å / Rmerge(I) obs: 0.525 / Mean I/σ(I) obs: 2 / % possible all: 92.3

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Phasing

PhasingMethod: MAD
Phasing set
ID
1
2
3
Phasing MAD set
Clust-IDExpt-IDSet-IDWavelength (Å)F double prime refinedF prime refined
13 wavelength10.91954.98-6.73
13 wavelength20.91983.08-8.81
13 wavelength30.90933.95-2.01
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1LAM116.7550.2240.7470.1660.17
2LAM121.6470.1060.2830.1290.345
3LAM138.8730.970.1830.130.407
4LAM130.7720.3970.9480.0290.288

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Processing

Software
NameVersionClassificationNB
SOLVE2.01phasing
CNSrefinement
PDB_EXTRACT3.004data extraction
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 1.9→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.212 1810 5 %RANDOM
Rwork0.182 ---
obs0.182 36163 100 %-
all-36163 --
Solvent computationBsol: 74.79 Å2
Displacement parametersBiso mean: 33.2 Å2
Baniso -1Baniso -2Baniso -3
1-7.11 Å20 Å20 Å2
2--7.11 Å20 Å2
3----14.22 Å2
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2517 0 6 471 2994
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.59
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.92
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM
X-RAY DIFFRACTION2ION.PARAM
X-RAY DIFFRACTION3WATER_REP.PARAM

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