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- PDB-1t70: Crystal structure of a novel phosphatase from Deinococcus radiodurans -

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Basic information

Entry
Database: PDB / ID: 1t70
TitleCrystal structure of a novel phosphatase from Deinococcus radiodurans
ComponentsPhosphatase
KeywordsHYDROLASE / Crystal / phosphatase / X-ray crystallography / Structural Genomics / Berkeley Structural Genomics Center / BSGC / PSI / Protein Structure Initiative
Function / homology
Function and homology information


phosphoenolpyruvate phosphatase / phosphoenolpyruvate phosphatase activity / 2',3'-cyclic-nucleotide 2'-phosphodiesterase / 2',3'-cyclic-nucleotide 2'-phosphodiesterase activity / 2',3'-cyclic-nucleotide 3'-phosphodiesterase activity / metal ion binding
Similarity search - Function
Metallophosphoesterase, YmdB-like / YmdB-like protein / Metallo-dependent phosphatases / Purple Acid Phosphatase; chain A, domain 2 / Metallo-dependent phosphatase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Phosphatase/phosphodiesterase DR_1281
Similarity search - Component
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsShin, D.H. / Wang, W. / Kim, R. / Yokota, H. / Kim, S.H. / Berkeley Structural Genomics Center (BSGC)
CitationJournal: Proteins / Year: 2008
Title: Structural and enzymatic characterization of DR1281: A calcineurin-like phosphoesterase from Deinococcus radiodurans.
Authors: Shin, D.H. / Proudfoot, M. / Lim, H.J. / Choi, I.K. / Yokota, H. / Yakunin, A.F. / Kim, R. / Kim, S.H.
History
DepositionMay 7, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Jan 30, 2013Group: Other
Revision 1.4Oct 11, 2017Group: Refinement description / Category: software
Revision 1.5Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_related
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_related.db_name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphatase
B: Phosphatase
C: Phosphatase
D: Phosphatase
E: Phosphatase
F: Phosphatase
G: Phosphatase
H: Phosphatase


Theoretical massNumber of molelcules
Total (without water)223,7728
Polymers223,7728
Non-polymers00
Water5,747319
1
A: Phosphatase
B: Phosphatase


Theoretical massNumber of molelcules
Total (without water)55,9432
Polymers55,9432
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3260 Å2
ΔGint-17 kcal/mol
Surface area19350 Å2
MethodPISA
2
C: Phosphatase
D: Phosphatase


Theoretical massNumber of molelcules
Total (without water)55,9432
Polymers55,9432
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3260 Å2
ΔGint-18 kcal/mol
Surface area19340 Å2
MethodPISA
3
E: Phosphatase
F: Phosphatase


Theoretical massNumber of molelcules
Total (without water)55,9432
Polymers55,9432
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3260 Å2
ΔGint-18 kcal/mol
Surface area19370 Å2
MethodPISA
4
G: Phosphatase
H: Phosphatase


Theoretical massNumber of molelcules
Total (without water)55,9432
Polymers55,9432
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3280 Å2
ΔGint-16 kcal/mol
Surface area19420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)242.793, 116.614, 89.283
Angle α, β, γ (deg.)90.00, 109.40, 90.00
Int Tables number5
Cell settingmonoclinic
Space group name H-MC121

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Components

#1: Protein
Phosphatase / conserved hypothetical protein


Mass: 27971.512 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Details: phosphatase activity aginst p-nitrophenylphosphate
Source: (gene. exp.) Deinococcus radiodurans (radioresistant)
Strain: R1 / Plasmid: PSJS1244 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9RUV0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 319 / 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: 2.67 Å3/Da / Density % sol: 52.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 10.5
Details: n-hexyl beta-D glucose, PEG 4000, CAPS, Lithium Sulfate, pH 10.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 16, 2003 / Details: Monochromator
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.3→111.8 Å / Num. all: 205986 / Num. obs: 194039 / % possible obs: 94.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 16.9 Å2
Reflection shellResolution: 2.3→2.34 Å / % possible all: 58.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
SnBphasing
CNS1.1refinement
HKL-2000data reduction
RefinementMethod to determine structure: SAD / Resolution: 2.3→19.95 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 113819.34 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.26 8149 10 %RANDOM
Rwork0.207 ---
all0.212 ---
obs0.2071 81627 78.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 34.5226 Å2 / ksol: 0.319787 e/Å3
Displacement parametersBiso mean: 43.4 Å2
Baniso -1Baniso -2Baniso -3
1--4.58 Å20 Å2-14.67 Å2
2--13.71 Å20 Å2
3----9.13 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.38 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 2.3→19.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15776 0 0 319 16095
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d25.3
X-RAY DIFFRACTIONc_improper_angle_d0.83
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.316 732 10.1 %
Rwork0.264 6526 -
obs--42.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
X-RAY DIFFRACTION3ION.PARAM

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