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- PDB-4jst: Structure of Clostridium thermocellum polynucleotide kinase bound... -

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Basic information

Entry
Database: PDB / ID: 4jst
TitleStructure of Clostridium thermocellum polynucleotide kinase bound to UTP
ComponentsMetallophosphoesterase
KeywordsTRANSFERASE / RNA repair / P-loop phosphotransferase / polynucleotide kinase
Function / homology
Function and homology information


hydrolase activity / carbohydrate metabolic process / GTP binding / ATP binding / metal ion binding
Similarity search - Function
Polynucleotide kinase-phosphatase, bacterial / PrpE-like, metallophosphatase domain / Polynucleotide kinase-phosphatase, ligase domain / PNKP adenylyltransferase domain, ligase domain / AAA domain / Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like / P-loop containing nucleotide triphosphate hydrolases ...Polynucleotide kinase-phosphatase, bacterial / PrpE-like, metallophosphatase domain / Polynucleotide kinase-phosphatase, ligase domain / PNKP adenylyltransferase domain, ligase domain / AAA domain / Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
URIDINE 5'-TRIPHOSPHATE / Metallophosphoesterase
Similarity search - Component
Biological speciesClostridium thermocellum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Direct refinement / Resolution: 2.03 Å
AuthorsDas, U. / Wang, L.K. / Smith, P. / Shuman, S.
CitationJournal: Biochemistry / Year: 2013
Title: Structural and biochemical analysis of the phosphate donor specificity of the polynucleotide kinase component of the bacterial pnkphen1 RNA repair system.
Authors: Das, U. / Wang, L.K. / Smith, P. / Shuman, S.
History
DepositionMar 22, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Metallophosphoesterase
B: Metallophosphoesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3627
Polymers39,3222
Non-polymers1,0405
Water4,792266
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3550 Å2
ΔGint-49 kcal/mol
Surface area16310 Å2
Unit cell
Length a, b, c (Å)45.306, 66.781, 119.546
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Metallophosphoesterase


Mass: 19661.062 Da / Num. of mol.: 2 / Mutation: V44M, L137M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium thermocellum (bacteria) / Strain: ATCC 27405 / DSM 1237 / Gene: Cthe_2768 / Production host: Escherichia coli (E. coli)
References: UniProt: A3DJ38, polynucleotide 5'-hydroxyl-kinase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-UTP / URIDINE 5'-TRIPHOSPHATE / Uridine triphosphate


Mass: 484.141 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H15N2O15P3 / Comment: UTP*YM
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 266 / 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: 2.3 Å3/Da / Density % sol: 46.51 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 100mM sodium citrate, 100mM MgCl2, 16-18% PEG 3350, 2mM UTP, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 130 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 26, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.03→46.1 Å / Num. all: 24709 / Num. obs: 24709 / % possible obs: 100 % / Observed criterion σ(F): -999 / Observed criterion σ(I): -999
Reflection shellResolution: 2.03→2.08 Å / % possible all: 100

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Processing

Software
NameVersionClassification
CBASSdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8.1_1168)refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: Direct refinement / Resolution: 2.03→44.538 Å / SU ML: 0.21 / σ(F): 1.34 / Phase error: 23.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2244 1901 7.89 %
Rwork0.1701 --
obs0.1745 24105 99.76 %
all-24153 -
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.03→44.538 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2738 0 61 266 3065
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092867
X-RAY DIFFRACTIONf_angle_d1.263881
X-RAY DIFFRACTIONf_dihedral_angle_d17.1891117
X-RAY DIFFRACTIONf_chiral_restr0.072439
X-RAY DIFFRACTIONf_plane_restr0.005491
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.03-2.08090.27281330.19391538X-RAY DIFFRACTION99
2.0809-2.13720.26531320.20641551X-RAY DIFFRACTION100
2.1372-2.20.24411310.1891546X-RAY DIFFRACTION100
2.2-2.27110.27281350.18921574X-RAY DIFFRACTION100
2.2711-2.35220.29451330.1891549X-RAY DIFFRACTION100
2.3522-2.44640.28211370.18211580X-RAY DIFFRACTION100
2.4464-2.55770.24231340.18711569X-RAY DIFFRACTION100
2.5577-2.69260.26191340.191569X-RAY DIFFRACTION100
2.6926-2.86120.22331340.17811574X-RAY DIFFRACTION100
2.8612-3.08210.22091360.18471590X-RAY DIFFRACTION100
3.0821-3.39220.24621370.17131596X-RAY DIFFRACTION100
3.3922-3.88280.2181380.16081613X-RAY DIFFRACTION100
3.8828-4.89090.15291400.13181630X-RAY DIFFRACTION100
4.8909-44.54890.19661470.15811725X-RAY DIFFRACTION100

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