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- PDB-8sbo: Crystal Structure of Dephospho-CoA kinase from Klebsiella aerogen... -

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Basic information

Entry
Database: PDB / ID: 8sbo
TitleCrystal Structure of Dephospho-CoA kinase from Klebsiella aerogenes (P21 Form 2)
ComponentsDephospho-CoA kinase
KeywordsTRANSFERASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE
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 nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Dephospho-CoA kinase
Similarity search - Component
Biological speciesKlebsiella aerogenes KCTC 2190 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93022C00036 United States
National Institutes of Health/Office of the DirectorOD030394 United States
CitationJournal: To be published
Title: Crystal Structure of Dephospho-CoA kinase from Klebsiella aerogenes (P21 Form 2)
Authors: Liu, L. / Lovell, S. / Battaile, K.P. / Seibold, S.
History
DepositionApr 3, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 12, 2023Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0076
Polymers47,7002
Non-polymers3074
Water6,305350
1
A: Dephospho-CoA kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0043
Polymers23,8501
Non-polymers1542
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Dephospho-CoA kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0043
Polymers23,8501
Non-polymers1542
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.841, 48.827, 64.266
Angle α, β, γ (deg.)90.00, 96.86, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 23850.084 Da / Num. of mol.: 2 / Mutation: G2T, V127I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella aerogenes KCTC 2190 (bacteria)
Gene: coaE, EAE_11320 / Plasmid: KlaeA.00139.a.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0H3FR62, dephospho-CoA kinase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 350 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.08 Å3/Da / Density % sol: 41 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Morpheus H4: 12.5%(v/v) MPD, 12.5%(v/v) PEG 1000, 12.5%(w/v) PEG 3350, 100 mM Imidazole/MES, pH 6.5, 20 mM DL-Glutamic acid, 20 mM DL-Alanine; 20 mM Glycine, 20 mM DL-Lysine ...Details: Morpheus H4: 12.5%(v/v) MPD, 12.5%(v/v) PEG 1000, 12.5%(w/v) PEG 3350, 100 mM Imidazole/MES, pH 6.5, 20 mM DL-Glutamic acid, 20 mM DL-Alanine; 20 mM Glycine, 20 mM DL-Lysine monohydrochloride and 20 mM DL-Serine. KlaeA.00139.a.B1.PW39166 at 24.8 mg/mL. Plate: 13153, well H4 drop 1, Puck: PSL-1416, Cryo: Direct

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Feb 14, 2022
RadiationMonochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.4→63.81 Å / Num. obs: 77530 / % possible obs: 100 % / Redundancy: 6.8 % / CC1/2: 1 / Rmerge(I) obs: 0.043 / Rpim(I) all: 0.017 / Rrim(I) all: 0.047 / Χ2: 0.97 / Net I/σ(I): 16.2 / Num. measured all: 529323
Reflection shellResolution: 1.4→1.44 Å / % possible obs: 100 % / Redundancy: 6.8 % / Rmerge(I) obs: 1.121 / Num. measured all: 38647 / Num. unique obs: 5715 / CC1/2: 0.774 / Rpim(I) all: 0.461 / Rrim(I) all: 1.214 / Χ2: 0.98 / Net I/σ(I) obs: 1.5

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Processing

Software
NameVersionClassification
PHENIX(1.21rc1_4918: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→21.17 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 22.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2104 3832 4.95 %
Rwork0.1731 --
obs0.1749 77423 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.4→21.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3125 0 18 350 3493
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083266
X-RAY DIFFRACTIONf_angle_d0.9034446
X-RAY DIFFRACTIONf_dihedral_angle_d13.1241218
X-RAY DIFFRACTIONf_chiral_restr0.07518
X-RAY DIFFRACTIONf_plane_restr0.01589
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.420.311470.26122725X-RAY DIFFRACTION100
1.42-1.440.31231430.25112702X-RAY DIFFRACTION100
1.44-1.460.31941550.24832676X-RAY DIFFRACTION100
1.46-1.480.29561560.22222677X-RAY DIFFRACTION100
1.48-1.50.26551210.20842756X-RAY DIFFRACTION100
1.5-1.520.25131660.19582716X-RAY DIFFRACTION100
1.52-1.550.23951150.18032682X-RAY DIFFRACTION100
1.55-1.570.21861370.18592732X-RAY DIFFRACTION100
1.57-1.60.22731530.17542696X-RAY DIFFRACTION100
1.6-1.630.23951480.16822713X-RAY DIFFRACTION100
1.63-1.670.21021200.16542729X-RAY DIFFRACTION100
1.67-1.70.22881490.16162703X-RAY DIFFRACTION100
1.7-1.740.19741260.16492755X-RAY DIFFRACTION100
1.74-1.790.20221220.15932730X-RAY DIFFRACTION100
1.79-1.830.23181430.16822697X-RAY DIFFRACTION100
1.83-1.890.19641230.17532760X-RAY DIFFRACTION100
1.89-1.950.21961490.18032715X-RAY DIFFRACTION100
1.95-2.020.21161500.17512718X-RAY DIFFRACTION100
2.02-2.10.2121370.16782698X-RAY DIFFRACTION100
2.1-2.20.20661570.1612715X-RAY DIFFRACTION100
2.2-2.310.21481570.15862719X-RAY DIFFRACTION100
2.31-2.460.20971690.16212732X-RAY DIFFRACTION100
2.46-2.640.19351630.16412693X-RAY DIFFRACTION100
2.64-2.910.20571260.17392781X-RAY DIFFRACTION100
2.91-3.330.20991370.17362751X-RAY DIFFRACTION100
3.33-4.190.18181310.16172780X-RAY DIFFRACTION100
4.19-21.170.20941320.18462840X-RAY DIFFRACTION99

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