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- PDB-6n39: Crystal structure of an dephospho-CoA kinase CoaE from Mycobacter... -

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Basic information

Entry
Database: PDB / ID: 6n39
TitleCrystal structure of an dephospho-CoA kinase CoaE from Mycobacterium paratuberculosis
ComponentsDephospho-CoA kinase
KeywordsTRANSFERASE / SSGCID / dephospho-CoA kinase / CoaE / 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
GrpB/Dephospho-CoA kinase / GrpB protein / Dephospho-CoA kinase / Dephospho-CoA kinase / Dephospho-CoA kinase (DPCK) domain profile. / Nucleotidyltransferase superfamily / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Dephospho-CoA kinase
Similarity search - Component
Biological speciesMycobacterium paratuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.15 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal structure of an dephospho-CoA kinase CoaE from Mycobacterium paratuberculosis
Authors: Mayclin, S.J. / Irwin, R.M. / Abendroth, J. / Horanyi, P.S. / Lorimer, D.D. / Edwards, T.E.
History
DepositionNov 14, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)45,5907
Polymers45,2361
Non-polymers3546
Water5,405300
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)85.170, 85.170, 198.780
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-699-

HOH

21A-759-

HOH

31A-816-

HOH

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Components

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


Mass: 45236.008 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium paratuberculosis (strain ATCC BAA-968 / K-10) (bacteria)
Strain: ATCC BAA-968 / K-10 / Gene: coaE, MAP_1326 / Plasmid: MypA.19484.a.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q740M4, dephospho-CoA kinase
#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 300 / 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: 3.99 Å3/Da / Density % sol: 69 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: SaltRX H9 opt (290572d2): 100 mM Bis-Tris Propane HCl pH 6.5, 4 M Ammonium acetate: MypaA.19484.a.B1.PW38003 at 19.5 mg/mL: direct cryo: puck id mae2-10

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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: Aug 4, 2017
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 40765 / % possible obs: 100 % / Redundancy: 9.565 % / Biso Wilson estimate: 46.251 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.063 / Rrim(I) all: 0.067 / Χ2: 1.034 / Net I/σ(I): 21.24
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.15-2.219.8520.5844.0129330.920.617100
2.21-2.279.8330.4864.8228860.9480.513100
2.27-2.339.8540.3846.0227940.9590.406100
2.33-2.49.8470.2927.8327400.9770.308100
2.4-2.489.8430.2419.2626300.9840.254100
2.48-2.579.8070.19111.3425830.9910.202100
2.57-2.679.7820.14814.2724890.9950.156100
2.67-2.789.7930.13316.0523700.9950.141100
2.78-2.99.740.10919.323080.9960.115100
2.9-3.049.6510.08423.8822110.9970.089100
3.04-3.219.5620.06828.8720910.9980.071100
3.21-3.49.4270.05932.6220120.9980.063100
3.4-3.639.330.04937.918730.9990.052100
3.63-3.939.2470.04540.2717590.9990.048100
3.93-4.39.1340.04242.7216470.9990.045100
4.3-4.819.1660.0444.3314900.9990.043100
4.81-5.559.1170.03844.4913270.9990.04100
5.55-6.88.9140.03943.1611480.9990.042100
6.8-9.628.5750.03445.59210.9990.036100
9.62-39.1437.0890.03541.325530.9980.03896.5

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACT3.24data extraction
PHASERphasing
BUCCANEERphasing
ARP/wARPmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.15→45 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.12
RfactorNum. reflection% reflection
Rfree0.1928 1981 4.87 %
Rwork0.1697 --
obs0.1708 40667 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 164.07 Å2 / Biso mean: 54.0214 Å2 / Biso min: 22.17 Å2
Refinement stepCycle: final / Resolution: 2.15→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3021 0 24 308 3353
Biso mean--56.06 50.78 -
Num. residues----404
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.15-2.20380.20971410.18962689
2.2038-2.26340.20821380.1812712
2.2634-2.330.19451450.17732704
2.33-2.40520.20181440.16782711
2.4052-2.49110.22281290.18242736
2.4911-2.59080.22931260.17472737
2.5908-2.70870.23061540.18312706
2.7087-2.85150.20271290.19832761
2.8515-3.03010.23761360.1972766
3.0301-3.26390.1991530.18832748
3.2639-3.59220.19061420.17172779
3.5922-4.11150.17691510.15112787
4.1115-5.17810.16461390.14092845
5.1781-500.18431540.17233005
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.5438-1.07050.67953.2146-1.47397.366-0.0876-0.3684-0.21341.03490.2056-0.16340.34270.4984-0.11040.62030.04880.01370.2869-0.00290.306967.8997-3.166342.7445
24.7709-1.19164.0694.3499-3.86246.17971.4309-1.7671-1.31412.528-0.6245-0.33652.0559-0.952-0.48621.5758-0.3439-0.28141.01060.25941.101374.1091-10.409966.2065
37.79261.8701-3.38426.8397-2.93869.52730.7453-0.9751-0.17251.4336-0.66630.4068-0.84480.47690.01050.7992-0.1137-0.03030.4914-0.07680.470576.2218-0.057556.2322
42.3096-0.10630.08372.8981.54082.2793-0.4275-0.5288-0.50510.97550.12390.55130.9203-0.25560.13930.7667-0.00550.23180.37690.11180.445255.6468-3.349845.2268
51.9425-0.7188-0.42752.46511.19670.9365-0.12120.28320.1146-0.37520.17970.07350.1256-0.0309-0.05220.4373-0.03430.00770.30660.02340.265560.16156.151527.7508
61.5189-0.2597-0.47813.2041-0.72162.59840.0220.02570.1305-0.04080.04260.1855-0.0906-0.116-0.05410.2350.0086-0.00240.2149-0.0030.234759.898327.610935.8514
72.65280.9579-0.25124.67320.30725.7509-0.01220.13120.0009-0.42920.14550.5835-0.1882-0.5659-0.07940.28910.0423-0.03210.33140.09420.410147.359933.408727.4435
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 39 )A-1 - 39
2X-RAY DIFFRACTION2chain 'A' and (resid 40 through 76 )A40 - 76
3X-RAY DIFFRACTION3chain 'A' and (resid 77 through 101 )A77 - 101
4X-RAY DIFFRACTION4chain 'A' and (resid 102 through 178 )A102 - 178
5X-RAY DIFFRACTION5chain 'A' and (resid 179 through 219 )A179 - 219
6X-RAY DIFFRACTION6chain 'A' and (resid 220 through 340 )A220 - 340
7X-RAY DIFFRACTION7chain 'A' and (resid 341 through 407 )A341 - 407

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