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- PDB-8dv0: Crystal Structure of a Dephospho-CoA kinase from Rickettsia felis -

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Basic information

Entry
Database: PDB / ID: 8dv0
TitleCrystal Structure of a Dephospho-CoA kinase from Rickettsia felis
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 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 speciesRickettsia felis URRWXCal2 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: to be published
Title: Crystal Structure of a Dephospho-CoA kinase from Rickettsia felis
Authors: Mayclin, S.J. / Abendroth, J. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionJul 27, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dephospho-CoA kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4555
Polymers23,1391
Non-polymers3164
Water3,243180
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.130, 39.680, 42.850
Angle α, β, γ (deg.)107.050, 106.870, 108.300
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 23138.959 Da / Num. of mol.: 1 / Fragment: RifeA.01444.a.B1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rickettsia felis URRWXCal2 (bacteria) / Strain: ATCC VR-1525 / URRWXCal2 / Gene: coaE, RF_0177 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q4UN30, dephospho-CoA kinase
#2: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / 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: 2.2 Å3/Da / Density % sol: 44 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Wizard 3/4 D11 (307537d11): 100 mM MES/NaOH pH6.5, 200 mM Ammonium sulfate, 30% (w/v) PEG 5000 MME: RifeA.01444.a.B1.PW308220 @ 26.35 mg/mL: dephosphocoenzyme A @ 6.6mM (does not appear in ...Details: Wizard 3/4 D11 (307537d11): 100 mM MES/NaOH pH6.5, 200 mM Ammonium sulfate, 30% (w/v) PEG 5000 MME: RifeA.01444.a.B1.PW308220 @ 26.35 mg/mL: dephosphocoenzyme A @ 6.6mM (does not appear in structure): cryoprotected in reservoir supplemented with 15% ethylene glycol: puck/pin id: psd0-3

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Oct 15, 2020 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.4→30.6 Å / Num. obs: 35777 / % possible obs: 95 % / Redundancy: 3.957 % / Biso Wilson estimate: 17.49 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.028 / Rrim(I) all: 0.032 / Χ2: 0.949 / Net I/σ(I): 23.76 / Num. measured all: 141563 / Scaling rejects: 3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.4-1.443.9860.6232.1310195277025580.7690.7292.3
1.44-1.483.9780.4363.0310192274725620.8880.50493.3
1.48-1.523.9760.2924.529816263924690.9370.33893.6
1.52-1.573.9790.2265.779586256124090.9620.26194.1
1.57-1.623.9710.1817.379209246423190.970.2194.1
1.62-1.673.9710.1488.979053241422800.9810.17194.4
1.67-1.743.9660.11311.828669230821860.9890.1394.7
1.74-1.813.960.0914.528426224521280.9920.10494.8
1.81-1.893.9540.06419.848082214620440.9960.07495.2
1.89-1.983.940.04925.547690204119520.9970.05795.6
1.98-2.093.9380.03732.277434197418880.9980.04395.6
2.09-2.213.9390.03139.716901182217520.9990.03696.2
2.21-2.373.9330.02743.56560172516680.9990.03196.7
2.37-2.563.9470.02546.636083159915410.9990.02896.4
2.56-2.83.9420.02252.075622147314260.9990.02696.8
2.8-3.133.930.0255.515200136213230.9990.02397.1
3.13-3.613.9480.01860.674572118711580.9990.02197.6
3.61-4.433.950.01763.273871100798010.01997.3
4.43-6.263.9360.01764.0429407647470.9990.0297.8
6.26-30.63.7780.0262.8814624213870.9990.02391.9

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX1.20.1_4487refinement
PDB_EXTRACT3.27data extraction
MR-Rosettaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4I1U

4i1u


Resolution: 1.4→30.6 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 20.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1986 2051 5.73 %
Rwork0.1562 33725 -
obs0.1587 35776 95.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 67.18 Å2 / Biso mean: 25.0737 Å2 / Biso min: 11.87 Å2
Refinement stepCycle: final / Resolution: 1.4→30.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1545 0 18 182 1745
Biso mean--37.49 37.41 -
Num. residues----192
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4-1.430.31771110.24292188229993
1.43-1.470.27851260.20592253237993
1.47-1.510.23851240.1652196232094
1.51-1.550.21521420.14772191233394
1.55-1.60.19191320.14252252238494
1.6-1.660.18851380.13732229236794
1.66-1.730.17751410.14622244238595
1.73-1.80.19421330.15852237237095
1.8-1.90.22771240.15872272239695
1.9-2.020.18081610.15292233239496
2.02-2.170.20111300.15132284241496
2.17-2.390.19091550.15022250240597
2.39-2.740.20451560.16522288244497
2.74-3.450.20851230.1632321244498
3.45-30.60.18511550.14832287244298

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