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- PDB-2if2: Crystal Structure of the Putative Dephospho-CoA Kinase from Aquif... -

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Basic information

Entry
Database: PDB / ID: 2if2
TitleCrystal Structure of the Putative Dephospho-CoA Kinase from Aquifex aeolicus, Northeast Structural Genomics Target QR72.
ComponentsDephospho-CoA kinase
KeywordsTRANSFERASE / alpha-beta protein / Structural Genomics / PSI-2 / 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 / ATP binding / cytoplasm
Similarity search - Function
Dephospho-CoA kinase / Dephospho-CoA kinase / Dephospho-CoA kinase (DPCK) domain profile. / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Dephospho-CoA kinase
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3 Å
AuthorsForouhar, F. / Hussain, M. / Seetharaman, J. / Hussain, A. / Wu, M. / Fang, Y. / Cunningham, K. / Ma, L.C. / Xiao, R. / Liu, J. ...Forouhar, F. / Hussain, M. / Seetharaman, J. / Hussain, A. / Wu, M. / Fang, Y. / Cunningham, K. / Ma, L.C. / Xiao, R. / Liu, J. / Baran, M. / Rost, B. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
History
DepositionSep 19, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance

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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)73,0387
Polymers72,6883
Non-polymers3504
Water1267
1
A: Dephospho-CoA kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3252
Polymers24,2291
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Dephospho-CoA kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3873
Polymers24,2291
Non-polymers1582
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Dephospho-CoA kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3252
Polymers24,2291
Non-polymers961
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.632, 97.013, 121.625
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 Dephospho-CoA kinase / Dephosphocoenzyme A kinase


Mass: 24229.205 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Strain: VF5 / Gene: coaE / Plasmid: pET21,JM109 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: O67792, dephospho-CoA kinase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 2.91 Å3/Da / Density % sol: 57.68 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.15
Details: 100mM cacodylate, 30% PEG8k, 210mM ammonium sulfate, and 5mM DTT., pH 6.15, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 18, 2006 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3→37.92 Å / Num. all: 32759 / Num. obs: 32628 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Biso Wilson estimate: 68.3 Å2 / Rmerge(I) obs: 0.101 / Rsym value: 0.067 / Net I/σ(I): 18.4
Reflection shellResolution: 3→3.1 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.653 / Mean I/σ(I) obs: 2.6 / Num. unique all: 3298 / Rsym value: 0.445 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
ADSCQUANTUMdata collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
XTALVIEWrefinement
RefinementMethod to determine structure: SAD / Resolution: 3→37.92 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 78145.85 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.284 2780 9.7 %RANDOM
Rwork0.235 ---
all0.239 32759 --
obs0.235 28597 87.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 20.9841 Å2 / ksol: 0.299129 e/Å3
Displacement parametersBiso mean: 65.8 Å2
Baniso -1Baniso -2Baniso -3
1-23.68 Å20 Å20 Å2
2---29.21 Å20 Å2
3---5.54 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.5 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.68 Å0.51 Å
Refinement stepCycle: LAST / Resolution: 3→37.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4541 0 19 7 4567
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d22.4
X-RAY DIFFRACTIONc_improper_angle_d0.73
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.396 358 10.4 %
Rwork0.335 3068 -
obs-3068 62.9 %

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