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- PDB-8u97: Crystal Structure of Dephospho-CoA kinase from Klebsiella aerogen... -

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Basic information

Entry
Database: PDB / ID: 8u97
TitleCrystal Structure of Dephospho-CoA kinase from Klebsiella aerogenes (AMP-PNP bound)
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 / 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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Dephospho-CoA kinase
Similarity search - Component
Biological speciesKlebsiella aerogenes KCTC 2190 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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 DirectorS10OD030394 United States
CitationJournal: To be published
Title: Crystal Structure of Dephospho-CoA kinase from Klebsiella aerogenes (AMP-PNP bound)
Authors: Liu, L. / Lovell, S. / Battaile, K.P. / Seibold, S.
History
DepositionSep 18, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 27, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dephospho-CoA kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3562
Polymers23,8501
Non-polymers5061
Water2,108117
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.306, 48.849, 63.878
Angle α, β, γ (deg.)90.00, 96.61, 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.: 1 / 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-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.1 Å3/Da / Density % sol: 41.41 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Morpheus E4: 12.5%(v/v) MPD, 12.5%(v/v) PEG 1000, 12.5%(w/v) PEG 3350, 100 mM Imidazole/MES, pH 6.5, 30 mM Diethylene glycol, 30 mM Triethyleneglycol, 30 mM Tetraethylene glycol and 30 mM ...Details: Morpheus E4: 12.5%(v/v) MPD, 12.5%(v/v) PEG 1000, 12.5%(w/v) PEG 3350, 100 mM Imidazole/MES, pH 6.5, 30 mM Diethylene glycol, 30 mM Triethyleneglycol, 30 mM Tetraethylene glycol and 30 mM Pentaethylene glycol. KlaeA.00139.a.B1.PW39166 at 24.8 mg/mL. 10 mM soak in AMP-PNP overnight. Plate: SS-Clover-3/17/23 wells H7, Puck: PSL-0116, 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: Jun 15, 2023
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: 1.5→63.45 Å / Num. obs: 31784 / % possible obs: 100 % / Redundancy: 6.8 % / CC1/2: 1 / Rmerge(I) obs: 0.036 / Rpim(I) all: 0.015 / Rrim(I) all: 0.039 / Χ2: 0.99 / Net I/σ(I): 19.4 / Num. measured all: 217334
Reflection shellResolution: 1.5→1.54 Å / % possible obs: 100 % / Redundancy: 7 % / Rmerge(I) obs: 0.933 / Num. measured all: 16525 / Num. unique obs: 2351 / CC1/2: 0.807 / Rpim(I) all: 0.378 / Rrim(I) all: 1.009 / Χ2: 0.99 / Net I/σ(I) obs: 1.9

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→24.42 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2204 1597 5.03 %
Rwork0.192 --
obs0.1934 31746 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.5→24.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1559 0 31 117 1707
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021663
X-RAY DIFFRACTIONf_angle_d0.5232275
X-RAY DIFFRACTIONf_dihedral_angle_d12.99619
X-RAY DIFFRACTIONf_chiral_restr0.041265
X-RAY DIFFRACTIONf_plane_restr0.006295
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.550.32531370.27292737X-RAY DIFFRACTION100
1.55-1.60.3171270.24392718X-RAY DIFFRACTION100
1.6-1.670.36221370.25322749X-RAY DIFFRACTION100
1.67-1.740.25691480.22762707X-RAY DIFFRACTION100
1.74-1.840.22341270.21072754X-RAY DIFFRACTION100
1.84-1.950.2531590.20442722X-RAY DIFFRACTION100
1.95-2.10.23441500.20152710X-RAY DIFFRACTION100
2.1-2.310.21661720.18082739X-RAY DIFFRACTION100
2.31-2.650.21111450.18422732X-RAY DIFFRACTION100
2.65-3.330.20851620.19292750X-RAY DIFFRACTION100
3.33-24.420.2081330.18282831X-RAY DIFFRACTION100

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