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- PDB-9bkz: Crystal Structure of Dephospho-CoA kinase from Klebsiella aerogen... -

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Basic information

Entry
Database: PDB / ID: 9bkz
TitleCrystal Structure of Dephospho-CoA kinase from Klebsiella aerogenes (CoA and ADP 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 / 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
ADENOSINE-5'-DIPHOSPHATE / COENZYME A / Dephospho-CoA kinase
Similarity search - Component
Biological speciesKlebsiella aerogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease / Seattle 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 (CoA and ADP bound)
Authors: Liu, L. / Lovell, S. / Battaile, K.P.
History
DepositionApr 29, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2024Provider: repository / Type: Initial release

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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)49,4406
Polymers47,7002
Non-polymers1,7404
Water21612
1
A: Dephospho-CoA kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1634
Polymers23,8501
Non-polymers1,3133
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Dephospho-CoA kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2772
Polymers23,8501
Non-polymers4271
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.096, 50.551, 70.595
Angle α, β, γ (deg.)90.00, 115.22, 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 (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-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-COA / COENZYME A / Coenzyme A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 2.37 Å3/Da / Density % sol: 48.15 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Morpheus F4: 12.5% v/v MPD; 12.5% PEG 1000; 12.5% w/v PEG 3350, 100 mM midazole/MES monohydrate (acid), pH 6.5, 20 mM D-Glucose; 20 mM D-Mannose; 20 mMD-Galactose; 20 mM L-Fucose; 20 mM D- ...Details: Morpheus F4: 12.5% v/v MPD; 12.5% PEG 1000; 12.5% w/v PEG 3350, 100 mM midazole/MES monohydrate (acid), pH 6.5, 20 mM D-Glucose; 20 mM D-Mannose; 20 mMD-Galactose; 20 mM L-Fucose; 20 mM D-Xylose; 20 mM N-Acetyl-D-Glucosamine. KlaeA.00139.a.B1.PW39166 at 24.8 mg/mL. Soak with 5mM ADP and 5 mM CoA in 18.75% v/v MPD; 18.75% PEG 1000; 18.75% w/v PEG 3350 for 10 days. Plate: Liu-S-118 Well G12 , Puck: PSL-0715, Cryo: 18.75% v/v MPD; 18.75% PEG 1000; 18.75% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9786 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Apr 13, 2024
RadiationMonochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.35→39.64 Å / Num. obs: 18892 / % possible obs: 99.9 % / Redundancy: 6.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.037 / Rrim(I) all: 0.096 / Χ2: 1.03 / Net I/σ(I): 11.8 / Num. measured all: 129858
Reflection shellResolution: 2.35→2.43 Å / % possible obs: 100 % / Redundancy: 6.9 % / Rmerge(I) obs: 1.154 / Num. measured all: 12786 / Num. unique obs: 1842 / CC1/2: 0.787 / Rpim(I) all: 0.471 / Rrim(I) all: 1.248 / Χ2: 1.02 / Net I/σ(I) obs: 1.6

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Processing

Software
NameVersionClassification
PHENIX(dev_5316: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→39.64 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 35.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2831 948 5.03 %
Rwork0.2313 --
obs0.234 18851 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.35→39.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3034 0 102 12 3148
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033184
X-RAY DIFFRACTIONf_angle_d0.6364342
X-RAY DIFFRACTIONf_dihedral_angle_d20.691213
X-RAY DIFFRACTIONf_chiral_restr0.041508
X-RAY DIFFRACTIONf_plane_restr0.005552
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.470.37131420.32782513X-RAY DIFFRACTION100
2.47-2.630.29961360.27322537X-RAY DIFFRACTION100
2.63-2.830.34621120.26292568X-RAY DIFFRACTION100
2.83-3.120.33611150.25332554X-RAY DIFFRACTION100
3.12-3.570.29781310.22632561X-RAY DIFFRACTION100
3.57-4.490.23241650.20512533X-RAY DIFFRACTION100
4.49-39.640.28441470.22322637X-RAY DIFFRACTION100
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)
11.4777-1.24371.09260.136-0.36730.8595-0.1714-0.15340.0535-0.01470.09060.050.1019-0.09420.06440.7543-0.0212-0.06040.34760.03220.4221-13.4611-3.0311-21.3863
25.18842.16823.9037.09283.8254.639-0.0710.6669-0.17410.42340.2434-0.7947-0.21091.85780.12750.8028-0.0248-0.01540.50130.11450.5937-5.83951.9676-27.6337
34.33596.282-0.598.7879-1.29553.5484-0.78350.59070.172-1.0230.74830.37350.1263-0.33750.01250.7210.0818-0.12040.5792-0.03590.5294-3.0523-11.266-11.3423
41.46210.7832-0.7274.8018-0.7162.10080.06530.0951-0.18960.06450.0765-0.03690.4093-0.1971-0.14660.54620.1026-0.11350.4066-0.01580.4188-0.9993-13.859-7.4677
51.7411-0.34290.09411.1401-2.32793.8670.13670.28910.15320.08940.25720.4975-0.7776-0.7935-0.43030.65090.2255-0.02410.6520.06950.5885-40.7855-2.6605-17.8349
66.5451-0.65210.87795.3217-0.70023.47340.4560.54210.20630.3257-0.24780.38780.3014-1.1731-0.25260.83690.0980.06080.85110.05770.5386-42.6165-1.5826-30.3882
72.1331.38860.06035.30051.14783.9307-0.15410.1627-0.1162-0.20470.2787-0.02720.1233-0.0951-0.07020.68420.0879-0.01140.48550.05230.4533-34.3385-14.2434-10.1879
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 77 )
2X-RAY DIFFRACTION2chain 'A' and (resid 78 through 101 )
3X-RAY DIFFRACTION3chain 'A' and (resid 102 through 145 )
4X-RAY DIFFRACTION4chain 'A' and (resid 146 through 202 )
5X-RAY DIFFRACTION5chain 'B' and (resid 2 through 54 )
6X-RAY DIFFRACTION6chain 'B' and (resid 55 through 101 )
7X-RAY DIFFRACTION7chain 'B' and (resid 102 through 202 )

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