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- PDB-1n3b: Crystal Structure of Dephosphocoenzyme A kinase from Escherichia coli -

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Basic information

Entry
Database: PDB / ID: 1n3b
TitleCrystal Structure of Dephosphocoenzyme A kinase from Escherichia coli
ComponentsDephospho-CoA kinase
KeywordsTRANSFERASE / trimer / P-loop / alpha/beta / Montreal-Kingston Bacterial Structural Genomics Initiative / BSGI / Structural Genomics
Function / homology
Function and homology information


dephospho-CoA kinase / dephospho-CoA kinase activity / coenzyme A biosynthetic process / phosphorylation / ATP binding / cytoplasm
Similarity search - Function
Dephospho-CoA kinase / Dephospho-CoA kinase / Dephospho-CoA kinase (DPCK) domain profile. / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Dephospho-CoA kinase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsO'Toole, N. / Barbosa, J.A.R.G. / Li, Y. / Hung, L.-W. / Matte, A. / Cygler, M. / Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI)
Citation
Journal: Protein Sci. / Year: 2003
Title: Crystal Structure of a Trimeric Form of Dephosphocoenzyme A Kinase from Escherichia coli
Authors: O'Toole, N. / Barbosa, J.A.R.G. / Li, Y. / Hung, L.-W. / Matte, A. / Cygler, M.
#1: Journal: J.Struct.Biol. / Year: 2001
Title: Crystal Structure of Dephospho-coenzyme A Kinase from Haemophilus influenzae
Authors: Oblomova, G. / Teplyakov, A. / Bonander, N. / Eisenstein, E. / Howard, A. / Gilliland, G.
#2: Journal: J.Bacteriol. / Year: 2001
Title: Identification of yace (coaE) as the Structural Gene for Dephosphocoenzyme A Kinase in Escherichia coli K-12
Authors: Mishra, P.K. / Park, P.K. / Drueckhammer, D.G.
#3: Journal: J.Mol.Biol. / Year: 1998
Title: The structure of a Trimeric Archael Adenylate Kinase
Authors: Vorhein, C. / Bonisch, H. / Schafer, G. / Schulz, G.E.
#4: Journal: Biochem.J. / Year: 1983
Title: A Bifunctional Enzyme Complex in Coenzyme A Biosynthesis: Purification of Pantetheine Phosphate Adenylyltransferase and Dephospho-CoA Kinase
Authors: Worral, D.M. / Tubbs, P.K.
#5: Journal: Biochem.J. / Year: 2002
Title: Identification and Characterization of the Gene Encoding the Human Adenylyltransferase and Dephosphocoenzyme A Kinase Bifunctional Enzyme
Authors: Aghajanian, S. / Worral, D.M.
History
DepositionOct 25, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 28, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 16, 2014Group: Data collection
Revision 1.4Feb 1, 2017Group: Structure summary

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dephospho-CoA kinase
B: Dephospho-CoA kinase
C: Dephospho-CoA kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,07413
Polymers72,1133
Non-polymers96110
Water8,089449
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6690 Å2
ΔGint-165 kcal/mol
Surface area29430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.500, 82.410, 76.000
Angle α, β, γ (deg.)90.00, 94.77, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Dephospho-CoA kinase / Dephosphocoenzyme A kinase


Mass: 24037.652 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: COAE / Plasmid: pET20b derivative / Production host: Escherichia coli (E. coli) / Strain (production host): DL41(DE3) / References: UniProt: P0A6I9, dephospho-CoA kinase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 449 / 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: 2.45 Å3/Da / Density % sol: 49.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 8000, cacodylate buffer, ammonium sulfate, glycerol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 21 ℃ / pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mMTris-Cl1droppH7.5
20.2 M1dropNaCl
35 %(v/v)glycerol1drop
410 mMdithiothreitol1drop
59.3 mg/mlprotein1drop
620 %(w/v)PEG80001reservoir
750 mMcacodylate1reservoirpH6.5
80.2 Mammonium sulfate1reservoir
95 %(v/v)glycerol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.97957, 0.97941
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 4, 2001 / Details: monochromating crystal
RadiationMonochromator: graphite / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979571
20.979411
ReflectionResolution: 1.8→40 Å / Num. obs: 59512 / % possible obs: 86.3 % / Redundancy: 6.7 % / Rsym value: 0.065 / Net I/σ(I): 26.1
Reflection shellResolution: 1.81→1.88 Å / Num. unique all: 5096 / Rsym value: 0.439 / % possible all: 74.3
Reflection
*PLUS
Lowest resolution: 40 Å / Num. obs: 56459 / % possible obs: 88.7 % / Num. measured all: 380533 / Rmerge(I) obs: 0.063
Reflection shell
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 1.87 Å / % possible obs: 71.1 % / Rmerge(I) obs: 0.546

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
CNS1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 1.8→40 Å / Isotropic thermal model: isotropic / Cross valid method: Free-R / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: Bulk solvent correction employed. The structure was refined using Friedel's pairs.
RfactorNum. reflection% reflectionSelection details
Rfree0.246 5518 4.4 %Random
Rwork0.217 ---
obs-107923 86.8 %-
Displacement parametersBiso mean: 28.46 Å2
Refinement stepCycle: LAST / Resolution: 1.8→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4547 0 50 449 5046
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.26
X-RAY DIFFRACTIONc_bond_d0.008
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 40 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_bond_d / Dev ideal: 0.008

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