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- PDB-1t3h: X-ray Structure of Dephospho-CoA Kinase from E. coli Norteast Str... -

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Basic information

Entry
Database: PDB / ID: 1t3h
TitleX-ray Structure of Dephospho-CoA Kinase from E. coli Norteast Structural Genomics Consortium Target ER57
ComponentsDephospho-CoA kinase
KeywordsTRANSFERASE / structural genomics / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
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 / SAD / Resolution: 2.5 Å
AuthorsKuzin, A.P. / Chen, Y. / Forouhar, F. / Edstrom, W. / Benach, J. / Vorobiev, S. / Acton, T. / Shastry, R. / Ma, L.-C. / Xia, R. ...Kuzin, A.P. / Chen, Y. / Forouhar, F. / Edstrom, W. / Benach, J. / Vorobiev, S. / Acton, T. / Shastry, R. / Ma, L.-C. / Xia, R. / Montelione, G. / Tong, L. / Hunt, J. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: TO BE PUBLISHED
Title: X-ray Structure of Dephospho-CoA Kinase from E. coli Norteast Structural Genomics Consortium Target ER57
Authors: Kuzin, A.P. / Chen, Y. / Forouhar, F. / Edstrom, W. / Benach, J. / Vorobiev, S. / Acton, T. / Shastry, R. / Ma, L.-C. / Xia, R. / Montelione, G. / Tong, L. / Hunt, J.
History
DepositionApr 26, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)71,7715
Polymers71,5793
Non-polymers1922
Water2,576143
1
A: Dephospho-CoA kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9562
Polymers23,8601
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Dephospho-CoA kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9562
Polymers23,8601
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Dephospho-CoA kinase


Theoretical massNumber of molelcules
Total (without water)23,8601
Polymers23,8601
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.630, 80.905, 75.454
Angle α, β, γ (deg.)90.00, 93.95, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 23859.500 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P0A6I9, dephospho-CoA kinase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 143 / 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: 2.5 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: 100 mM sodium acetate, 160 mM ammonium sulfate, 22% PEG 3350, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97932 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 2, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97932 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. obs: 45074 / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Biso Wilson estimate: 27.8 Å2 / Rmerge(I) obs: 0.081 / Rsym value: 0.081 / Net I/σ(I): 14.2

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→19.53 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 228923.74 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.284 2112 5.1 %RANDOM
Rwork0.238 ---
obs0.238 41372 91.2 %-
all-45157 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 18.62 Å2 / ksol: 0.287882 e/Å3
Displacement parametersBiso mean: 33.6 Å2
Baniso -1Baniso -2Baniso -3
1--3.3 Å20 Å2-6.05 Å2
2--2.04 Å20 Å2
3---1.26 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.37 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 2.5→19.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4650 0 10 143 4803
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.016
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_deg1.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.4
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
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.322 329 5.6 %
Rwork0.259 5571 -
obs--77.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP

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